Contacts of the helix formed by residues 99 - 117 (chain B) in PDB entry 1HHO
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
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Residue Dist Surf HB Arom Phob DC
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41B PHE* 5.2 1.0 - - - -
97B HIS 3.5 5.1 + - - -
98B VAL* 1.3 72.1 - - - +
100B PRO* 1.3 67.4 - - - +
101B GLU* 2.9 33.1 + - - +
102B ASN* 2.8 39.8 + - - +
145B TYR* 4.3 1.7 - - - -
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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 VAL 3.1 9.1 - - - +
99B ASP* 1.3 89.3 - - - +
101B GLU* 1.3 59.5 + - - +
102B ASN 3.2 1.6 - - - -
103B PHE* 3.1 32.5 - - + +
104B ARG* 2.7 25.6 + - - +
142B ALA* 3.5 22.9 - - + -
145B TYR* 3.2 32.8 - - + -
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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
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99A LYS* 4.1 19.8 + - - +
99B ASP* 2.9 17.0 + - - +
100B PRO* 1.3 75.1 - - - +
102B ASN* 1.3 61.4 + - - +
103B PHE 3.0 5.2 - - - -
104B ARG* 3.1 25.2 + - - +
105B LEU* 2.9 52.2 + - + +
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Residues in contact with ASN 102 (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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31B LEU* 4.5 1.5 - - + +
37B TRP* 2.9 35.1 + - - +
38B THR* 3.6 18.2 - - + +
41B PHE* 5.2 3.2 - - - -
98B VAL* 4.0 8.6 - - + +
99B ASP* 2.8 30.9 + - - +
101B GLU* 1.3 81.2 - - - +
103B PHE* 1.3 57.2 + - - +
105B LEU* 3.6 17.9 - - + +
106B LEU* 3.0 24.1 + - - +
147B HEM 3.1 30.6 - - + +
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Residues in contact with PHE 103 (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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92B HIS* 4.0 22.7 - + + -
98B VAL* 3.7 36.6 - - + -
100B PRO* 3.1 28.7 - - + +
101B GLU 3.0 0.2 - - - -
102B ASN* 1.3 80.7 - - - +
104B ARG* 1.3 56.5 - - - +
106B LEU* 4.1 1.6 - - - +
107B GLY* 3.2 20.4 + - - -
134B VAL 5.1 0.3 - - - +
138B ALA* 3.7 31.2 - - + +
141B LEU* 3.7 29.4 - - + -
142B ALA* 3.7 24.9 - - + -
145B TYR* 4.2 6.3 - + - -
147B HEM 3.8 37.2 - + + +
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Residues in contact with ARG 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* 2.7 41.6 + - - +
101B GLU* 3.1 28.1 + - - +
103B PHE* 1.3 74.2 - - - +
105B LEU* 1.3 65.2 + - + +
107B GLY* 3.2 2.0 + - - -
108B ASN* 2.7 40.9 + - - +
134B VAL* 5.8 3.1 - - + -
135B ALA* 5.9 3.7 - - - +
138B ALA* 3.8 26.1 + - + +
139B ASN* 2.6 35.8 + - - +
142B ALA* 4.6 5.9 - - - +
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Residues in contact with LEU 105 (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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31B LEU* 4.1 4.7 - - + -
35B TYR* 4.1 35.4 - - + +
37B TRP* 4.0 18.8 - - + -
101B GLU* 2.9 36.3 + - + +
102B ASN* 3.6 28.7 - - - +
104B ARG* 1.3 81.1 - - + +
106B LEU* 1.3 50.6 + - - +
108B ASN* 3.1 10.4 + - + +
109B VAL* 2.7 41.4 + - - +
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Residues in contact with LEU 106 (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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27B ALA* 3.8 26.0 - - + +
28B LEU* 4.1 8.5 - - + +
31B LEU* 3.6 26.0 - - + +
67B VAL* 3.8 17.9 - - + -
71B PHE* 5.0 4.5 - - + -
102B ASN 3.0 21.1 + - - +
103B PHE 4.1 3.6 - - - +
105B LEU* 1.3 66.5 - - - +
107B GLY* 1.4 57.5 + - - +
109B VAL* 2.9 7.5 + - + +
110B LEU* 2.6 38.9 + - + +
147B HEM 3.6 50.3 - - + -
150B OXY 4.3 4.9 - - - +
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Residues in contact with GLY 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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71B PHE* 4.9 6.8 - - - -
103B PHE 3.2 11.1 + - - -
104B ARG 3.2 5.9 + - - -
106B LEU* 1.4 78.6 - - - +
108B ASN* 1.3 57.1 + - - +
110B LEU* 3.0 9.5 + - - +
111B VAL* 3.0 21.7 + - - +
134B VAL* 3.3 39.8 - - - +
147B HEM 5.8 0.2 - - - -
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Residues in contact with ASN 108 (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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36A PHE* 5.2 3.6 - - - -
100A LEU* 6.0 1.6 - - - +
103A HIS* 3.1 41.3 + - + +
35B TYR* 5.7 3.4 - - - +
104B ARG* 2.7 27.7 + - - +
105B LEU* 3.5 11.4 - - + +
107B GLY* 1.3 71.0 - - - +
109B VAL* 1.3 63.7 + - + +
110B LEU 3.0 1.3 - - - -
111B VAL* 3.4 2.5 - - - +
112B CYS* 2.9 24.4 + - - -
131B GLN* 3.3 26.9 - - - +
134B VAL* 4.3 5.1 - - - +
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Residues in contact with VAL 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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122A HIS* 4.6 17.5 - - + +
27B ALA* 3.1 35.9 - - + +
30B ARG* 4.3 3.8 - - + +
31B LEU* 4.0 13.0 - - + +
35B TYR* 3.5 30.5 - - + +
105B LEU 2.7 30.2 + - - +
106B LEU* 3.6 15.0 - - + +
108B ASN* 1.3 72.6 - - + +
110B LEU* 1.3 62.7 + - - +
112B CYS* 3.0 9.9 + - - +
113B VAL* 2.8 32.9 + - - +
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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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15B TRP* 4.3 16.8 - - + -
23B VAL* 4.3 16.6 - - + -
27B ALA* 4.2 15.5 - - + -
68B LEU* 4.5 11.2 - - + -
71B PHE* 4.0 39.5 - - + -
106B LEU* 2.6 14.1 + - + +
107B GLY* 3.1 15.5 - - - +
109B VAL* 1.3 79.8 - - - +
111B VAL* 1.3 60.9 - - - +
113B VAL* 3.2 4.4 + - + -
114B LEU* 3.0 43.1 + - + +
130B TYR* 6.1 1.8 - - + -
134B VAL* 4.4 6.3 - - + -
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Residues in contact with VAL 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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103A HIS* 4.3 1.8 - - - +
107A VAL* 4.1 7.6 - - + -
107B GLY 3.0 15.2 + - - +
108B ASN 3.2 6.9 + - - +
109B VAL 3.0 0.6 - - - -
110B LEU* 1.3 78.7 - - + +
112B CYS* 1.3 65.5 + - - +
114B LEU* 3.5 8.4 + - + +
115B ALA* 2.9 22.5 + - - +
122B PHE* 3.7 24.6 - - + -
127B GLN* 4.1 10.1 - - + +
130B TYR* 4.6 14.6 - - + +
131B GLN* 3.2 35.2 - - - +
134B VAL* 4.1 14.8 - - + -
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Residues in contact with CYS 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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103A HIS* 4.2 9.4 - - - -
106A LEU* 4.4 9.4 - - - -
107A VAL* 4.1 29.8 - - - +
110A ALA* 4.1 3.3 - - - +
117A PHE* 4.8 8.3 - - + -
122A HIS* 4.0 29.4 - - + -
30B ARG* 5.8 0.4 - - - -
108B ASN 2.9 18.2 + - - -
109B VAL* 3.2 12.6 - - - +
111B VAL* 1.3 79.3 - - - +
113B VAL* 1.3 57.4 - - + +
115B ALA* 3.2 5.6 + - - +
116B HIS* 2.9 28.9 + - - +
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Residues in contact with VAL 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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23B VAL* 3.6 34.1 - - + +
26B GLU* 3.9 15.3 - - + +
27B ALA* 3.3 31.4 - - + +
30B ARG* 4.0 19.5 - - - +
109B VAL 2.8 22.5 + - - +
110B LEU* 3.6 7.9 - - + +
112B CYS* 1.3 68.7 - - - +
114B LEU* 1.3 61.9 - - - +
116B HIS* 3.4 5.3 + - - -
117B HIS* 3.0 44.5 + - + +
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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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14B LEU* 5.1 1.8 - - + -
15B TRP* 4.5 9.0 - - + -
18B VAL* 4.0 27.1 - - + -
23B VAL* 4.4 10.5 - - + -
110B LEU* 3.0 41.0 + - + +
111B VAL* 3.7 8.7 - - + +
113B VAL* 1.3 74.6 - - - +
115B ALA* 1.3 67.8 + - - +
117B HIS* 2.8 11.4 + - + -
118B PHE* 2.9 29.9 + - + +
122B PHE* 3.9 20.2 - - + -
130B TYR* 4.2 31.9 - - + -
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Residues in contact with ALA 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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107A VAL* 3.6 32.8 - - + +
110A ALA* 4.6 0.7 - - + -
111A ALA* 3.5 11.2 - - + -
111B VAL 2.9 18.8 + - - +
112B CYS 3.5 5.2 - - - +
114B LEU* 1.3 78.4 - - - +
116B HIS* 1.3 59.0 + - - +
119B GLY* 3.1 25.5 + - - -
122B PHE* 3.6 27.7 - - + -
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Residues in contact with HIS 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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110A ALA* 3.5 21.6 - - + +
114A PRO* 2.9 60.1 + - + +
117A PHE* 3.7 24.1 + + + -
26B GLU* 3.8 9.3 + - - -
30B ARG* 3.6 19.6 + - - -
112B CYS 2.9 17.0 + - - +
113B VAL* 3.6 7.0 - - - +
114B LEU 3.1 0.2 - - - -
115B ALA* 1.3 76.8 - - - +
117B HIS* 1.3 88.9 + + - +
119B GLY* 4.2 3.5 + - - -
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Residues in contact with HIS 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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19B ASN* 6.0 0.6 - - - +
22B GLU 4.8 3.4 - - - -
23B VAL* 3.6 25.2 - - + +
26B GLU* 3.3 35.3 + - + -
113B VAL* 3.0 35.0 + - + +
114B LEU* 2.8 5.6 + - + +
116B HIS* 1.3 107.9 + + - +
118B PHE* 1.3 78.3 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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