Contacts of the helix formed by residues 99 - 120 (chain B) in PDB entry 1H4L
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 1.3 72.0 - - - +
100B PRO* 1.3 69.3 - - - +
101B GLU* 2.7 22.1 + - - +
102B ILE* 2.4 51.7 + - + +
103B VAL 3.1 4.4 + - - -
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Residues in contact with PRO 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU 3.4 6.5 - - - +
99B ASP* 1.3 90.0 - - - +
101B GLU* 1.3 61.5 + - - +
102B ILE 3.2 0.2 - - - -
103B VAL* 3.5 15.1 - - + +
104B LYS* 3.3 22.5 + - - +
254B LYS* 4.4 31.2 - - + +
285B TYR* 4.6 1.4 + - - -
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Residues in contact with GLU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B ASP* 2.7 20.2 + - - +
100B PRO* 1.3 75.5 - - - +
102B ILE* 1.3 64.9 + - + +
104B LYS* 3.6 31.8 + - - +
105B SER* 3.1 22.3 + - - -
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Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B TYR* 3.5 18.6 - - - +
98B LEU* 3.7 28.5 - - + -
99B ASP* 2.4 43.0 + - + +
101B GLU* 1.3 73.1 - - + +
103B VAL* 1.3 65.0 + - - +
105B SER* 3.1 5.1 + - - +
106B PHE* 3.0 44.8 + - + +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 4.3 13.7 - - + +
99B ASP 3.1 10.6 + - - +
100B PRO* 3.5 16.2 - - + +
102B ILE* 1.3 79.1 - - - +
104B LYS* 1.3 63.6 + - - +
106B PHE* 3.4 2.4 + - - +
107B LEU* 3.0 22.5 + - - +
192B PHE* 3.5 33.0 - - + -
195B LEU* 3.9 37.4 - - + +
196B ALA* 4.1 15.7 - - + +
254B LYS* 5.0 5.4 - - + +
255B LEU* 4.6 4.0 - - + -
285B TYR* 3.5 3.8 - - - +
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B PRO 3.3 9.2 + - - +
101B GLU* 3.7 28.2 + - - +
103B VAL* 1.3 80.7 - - - +
105B SER* 1.3 57.9 + - - +
107B LEU 3.3 0.5 + - - -
108B PHE* 2.8 31.0 + - + +
256B ASN* 5.5 6.7 - - - +
285B TYR* 3.1 49.5 + - + +
286B PHE* 3.4 23.6 - - + -
287B SER* 4.7 17.7 + - - +
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Residues in contact with SER 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU 3.1 13.2 + - - -
102B ILE* 3.1 8.7 + - - -
104B LYS* 1.3 76.4 - - - +
106B PHE* 1.3 70.3 + - - +
108B PHE* 3.0 6.8 + - - +
109B GLN* 2.9 44.6 + - - +
138B GLY 4.3 4.0 + - - -
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Residues in contact with PHE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU* 4.3 1.3 - - + -
90B TYR* 3.8 27.6 - + - -
98B LEU* 4.2 0.4 - - + -
102B ILE* 3.0 38.9 + - + +
105B SER* 1.3 79.5 - - - +
107B LEU* 1.3 58.1 + - - +
109B GLN* 4.0 0.6 - - - -
110B LEU* 3.0 30.1 + - - +
134B ILE* 3.5 44.4 - - + -
138B GLY* 3.5 29.8 - - - -
140B LEU* 3.5 28.0 - - + +
195B LEU* 3.9 33.2 - - + +
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B VAL 3.0 19.5 + - - +
104B LYS* 3.8 4.5 - - - +
106B PHE* 1.3 75.4 - - - +
108B PHE* 1.3 65.1 + - - +
110B LEU* 4.3 15.5 - - + -
111B LEU* 3.1 41.6 + - + +
188B ALA* 4.9 4.0 - - + +
192B PHE* 3.3 62.1 - - + +
195B LEU* 4.3 6.0 - - + +
262B LEU* 4.2 9.6 - - + -
266B LEU* 5.1 4.5 - - + -
285B TYR* 3.9 10.1 - - + -
286B PHE* 3.7 11.0 - - + -
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Residues in contact with PHE 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B LYS* 2.8 19.5 + - + +
105B SER* 3.0 7.8 + - - +
107B LEU* 1.3 79.2 - - - +
109B GLN* 1.3 69.3 + - + +
111B LEU* 3.7 2.4 - - - +
112B LYS* 2.8 58.1 + - + +
281B LEU* 3.8 23.8 - - + +
286B PHE* 3.5 34.1 - + + -
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Residues in contact with GLN 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B ASN* 3.1 33.3 - - - +
105B SER* 2.9 32.9 + - - +
106B PHE* 4.3 0.8 - - - +
108B PHE* 1.3 83.1 - - + +
110B LEU* 1.3 61.4 + - - +
112B LYS* 3.5 8.1 - - + +
113B GLY* 2.7 25.1 + - - -
138B GLY 2.8 27.9 + - - -
139B GLU* 3.1 13.3 - - - +
140B LEU* 3.0 35.2 + - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B PHE 3.0 20.3 + - - +
107B LEU* 3.9 13.2 - - + +
109B GLN* 1.3 76.0 - - - +
111B LEU* 1.3 60.7 + - - +
113B GLY* 2.9 2.9 + - - -
114B LEU* 2.8 30.8 + - + +
127B LEU* 4.1 27.6 - - + -
132B LEU* 3.9 26.7 - - + -
140B LEU* 3.6 12.7 - - + +
142B LEU* 3.6 26.7 - - + -
188B ALA* 4.3 15.9 - - + -
191B ILE* 4.1 17.9 - - + -
195B LEU* 6.0 0.9 - - + -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B LEU* 3.1 40.7 + - + +
110B LEU* 1.3 79.6 - - + +
112B LYS* 1.3 57.7 + - - +
114B LEU* 4.5 5.6 - - + -
115B GLY* 2.7 28.1 + - - -
185B MET* 4.0 22.2 - - + -
188B ALA* 4.5 10.8 - - + -
262B LEU* 4.7 2.5 - - + -
266B LEU* 4.8 3.6 - - + -
277B ALA* 3.9 9.0 - - - +
280B ALA* 3.7 30.3 - - + -
281B LEU* 3.6 19.9 - - + +
286B PHE* 3.4 30.5 - - + -
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Residues in contact with LYS 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 3.8 21.0 + - + +
61B LYS* 6.3 1.2 - - - +
62B ASN* 3.5 18.1 - - - +
108B PHE* 2.8 45.7 + - + +
109B GLN* 3.5 6.1 - - + +
110B LEU 3.0 0.2 - - - -
111B LEU* 1.3 78.9 - - - +
113B GLY* 1.3 60.6 + - - +
115B GLY* 3.9 0.5 - - - -
116B PHE* 3.1 21.7 + - - +
281B LEU* 3.9 16.1 - - + +
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Residues in contact with GLY 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B HIS* 4.4 2.9 - - - -
62B ASN* 3.8 19.7 - - - +
63B ILE* 3.6 13.6 - - - +
109B GLN 2.7 18.5 + - - -
110B LEU 3.5 1.8 - - - -
112B LYS* 1.3 72.4 - - - +
114B LEU* 1.3 64.8 + - - +
116B PHE* 3.1 6.8 + - - +
117B CYS* 3.0 17.3 + - - -
142B LEU* 3.9 12.8 - - - -
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Residues in contact with LEU 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU* 2.8 21.3 + - + +
111B LEU* 4.3 5.4 - - + +
113B GLY* 1.3 69.3 - - - -
115B GLY* 1.3 67.2 + - - +
117B CYS* 2.9 9.3 + - + +
118B HIS* 2.9 41.6 + - + +
124B HIS* 4.5 7.2 - - + -
127B LEU* 3.9 24.2 - - + -
142B LEU* 3.9 23.2 - - + +
184B ASP* 3.5 37.0 - - + +
185B MET* 3.8 27.1 - - + -
188B ALA* 4.2 7.4 - - + -
277B ALA* 5.2 0.7 - - + -
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Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B LEU 2.7 22.4 + - - -
112B LYS* 3.9 1.6 - - - -
114B LEU* 1.3 77.8 - - - +
116B PHE* 1.3 58.2 + - - +
118B HIS* 3.5 3.2 + - - +
119B SER* 3.1 22.0 + - - -
277B ALA* 3.3 23.3 - - - +
278B GLU* 5.2 4.6 - - - +
281B LEU* 5.3 3.6 - - - -
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU 5.2 0.2 - - - -
58B LEU* 4.2 8.1 - - + -
59B LYS 3.6 36.8 - - - -
60B HIS* 3.6 26.2 - + + -
63B ILE* 3.6 19.5 - - + -
112B LYS 3.1 14.5 + - - +
113B GLY 3.4 8.3 - - - +
114B LEU 3.1 0.6 - - - -
115B GLY* 1.3 75.2 - - - +
117B CYS* 1.3 64.7 + - - +
119B SER* 2.8 26.8 + - - -
120B ARG* 3.1 40.5 + - + +
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Residues in contact with CYS 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B LEU* 4.3 12.3 - - - -
63B ILE* 3.3 31.0 - - - -
113B GLY 3.0 10.3 + - - -
114B LEU* 2.9 16.2 + - + +
116B PHE* 1.3 77.8 - - - +
118B HIS* 1.3 64.5 + - - +
120B ARG* 3.1 4.7 + - - +
121B ASN 3.1 4.9 + - - -
122B VAL* 2.9 37.6 + - + +
124B HIS* 5.7 3.1 - - - +
142B LEU* 4.9 4.7 - - - -
145B PHE* 3.6 30.7 - - - -
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Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B LEU* 2.9 38.1 + - + +
115B GLY* 3.8 6.5 - - - +
117B CYS* 1.3 77.8 - - - +
119B SER* 1.3 63.5 + - - +
121B ASN* 2.9 15.8 + - - +
122B VAL 3.7 12.2 + - - +
123B LEU* 4.5 1.1 - - + +
151B PHE* 4.0 7.7 - - - -
181B THR* 3.4 48.4 + - + +
184B ASP* 3.0 33.6 - - + +
185B MET* 4.1 7.7 - - + -
276B SER* 6.3 0.7 - - - -
277B ALA* 4.2 18.6 - - + -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLY 3.1 12.8 + - - -
116B PHE* 2.8 26.7 + - - -
118B HIS* 1.3 76.3 - - - +
120B ARG* 1.3 65.0 + - - +
121B ASN* 3.5 10.4 + - - -
278B GLU* 5.9 2.9 - - - -
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Residues in contact with ARG 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B GLU* 2.8 53.8 + - - +
58B LEU* 3.8 15.0 - - + -
116B PHE* 3.1 46.4 + - + +
117B CYS 3.1 4.5 + - - +
118B HIS 3.0 0.8 - - - -
119B SER* 1.3 82.2 - - - +
121B ASN* 1.3 73.0 + - - +
122B VAL* 3.6 0.4 - - - -
273E LEU* 3.6 30.7 - - + +
277E ALA* 4.2 2.5 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il