Contacts of the helix formed by residues 103 - 124 (chain B) in PDB entry 1HQ3
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 PRO 103 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A GLU* 3.5 43.1 - - + +
95A LYS* 4.5 20.9 - - + -
96A LEU* 4.2 20.2 - - + +
101B LEU 4.0 4.9 - - - +
102B LEU* 1.3 86.9 - - + +
104B GLY* 1.3 67.3 + - - +
105B GLU 3.2 0.5 + - - -
106B LEU* 3.0 20.9 + - + +
107B ALA 3.3 2.9 + - - -
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Residues in contact with GLY 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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92A GLU* 3.6 4.5 + - - -
102B LEU 3.8 2.6 + - - -
103B PRO* 1.3 67.9 - - - +
105B GLU* 1.3 66.2 + - - -
107B ALA* 3.2 7.3 + - - +
108B LYS* 3.2 24.8 + - - +
67D ARG* 4.5 28.1 + - - +
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Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A GLU* 2.8 24.6 + - - +
104B GLY* 1.3 70.8 - - - -
106B LEU* 1.3 63.9 + - - +
108B LYS* 3.1 24.6 + - - +
109B HIS* 3.0 52.0 + - + +
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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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57A TYR* 3.7 31.3 - - + +
58A LEU* 4.1 16.4 - - + -
61A GLU* 4.4 12.3 - - + +
90A ASP* 5.5 1.1 - - - +
92A GLU* 3.0 39.0 + - + +
93A LEU* 4.0 29.2 - - + +
96A LEU* 4.4 10.5 - - + -
102B LEU* 3.8 7.1 - - + +
103B PRO* 3.0 22.2 + - + +
105B GLU* 1.3 76.4 - - - +
107B ALA* 1.3 56.6 + - - +
110B ALA* 3.1 29.3 + - - +
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Residues in contact with ALA 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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98B VAL* 4.2 9.4 - - - +
99B ARG* 4.5 12.3 - - + +
102B LEU* 3.4 38.5 - - + +
103B PRO 3.3 2.2 + - - -
104B GLY* 3.2 10.5 + - - +
105B GLU 3.1 0.4 - - - -
106B LEU* 1.3 78.5 - - - +
108B LYS* 1.3 59.1 + - + +
110B ALA* 3.8 1.0 - - - +
111B VAL* 3.0 36.8 + - + +
67D ARG* 5.9 3.1 - - - +
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Residues in contact with LYS 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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99B ARG* 5.7 6.3 - - - +
104B GLY 3.2 14.9 + - - +
105B GLU* 3.1 32.1 + - - +
107B ALA* 1.3 78.6 - - + +
109B HIS* 1.3 65.0 + - + +
111B VAL* 3.5 5.8 + - - +
112B SER* 3.0 26.5 + - - -
67D ARG* 5.6 7.9 - - - +
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Residues in contact with HIS 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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57A TYR* 3.2 37.3 + - + +
61A GLU* 5.7 0.4 + - - -
105B GLU* 3.0 41.7 + - + +
108B LYS* 1.3 82.5 - - + +
110B ALA* 1.3 54.5 + - - +
112B SER* 3.0 9.4 + - - -
113B GLU* 2.7 37.7 + - - +
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Residues in contact with ALA 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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54A VAL* 3.9 20.2 - - + +
57A TYR* 3.9 18.5 - - + -
98B VAL* 3.9 9.6 - - + -
102B LEU* 3.8 20.6 - - + -
106B LEU 3.1 20.1 + - - +
107B ALA 3.8 2.9 - - - +
109B HIS* 1.3 75.0 - - - +
111B VAL* 1.3 53.5 + - - +
113B GLU* 3.1 4.6 + - - +
114B GLY* 2.7 32.7 + - - -
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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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50A TYR* 3.3 15.5 + - - +
95B GLN* 3.5 21.8 - - + +
98B VAL* 4.2 11.9 - - + -
99B ARG* 3.6 48.7 - - + +
107B ALA 3.0 21.2 + - - +
108B LYS* 3.7 5.4 - - - +
110B ALA* 1.3 75.5 - - - +
112B SER* 1.3 60.4 + - - +
115B THR* 2.9 37.3 + - - +
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Residues in contact with SER 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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108B LYS 3.0 15.6 + - - -
109B HIS* 3.2 12.6 - - - -
111B VAL* 1.3 79.1 - - - +
113B GLU* 1.3 59.3 + - - +
115B THR* 3.4 5.8 + - - +
116B LYS* 3.0 44.4 + - - +
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Residues in contact with GLU 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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23A LEU* 5.8 2.6 - - + +
53A ALA* 3.7 14.8 - - + +
57A TYR* 3.9 39.7 - - + +
109B HIS 2.7 18.1 + - - +
110B ALA* 3.1 5.6 + - - +
112B SER* 1.3 73.7 + - - +
114B GLY* 1.3 63.8 + - - +
116B LYS* 3.5 29.6 + - + +
117B ALA* 3.1 23.4 + - - +
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Residues in contact with GLY 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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50A TYR* 3.7 30.0 - - - -
53A ALA* 3.9 12.8 - - - +
54A VAL* 4.6 0.9 - - - +
110B ALA 2.7 18.8 + - - -
111B VAL 3.8 0.9 - - - -
113B GLU* 1.3 72.8 - - - +
115B THR* 1.3 63.2 + - - +
117B ALA* 3.1 5.7 + - - +
118B VAL* 3.1 24.6 + - - +
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Residues in contact with THR 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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50A TYR* 3.6 5.8 - - - -
95B GLN* 3.5 18.7 + - - -
111B VAL* 2.9 22.6 + - - +
112B SER* 3.7 7.6 - - - +
114B GLY* 1.3 75.1 - - - +
116B LYS* 1.3 63.1 + - - +
118B VAL* 3.3 5.5 + - - +
119B THR* 2.9 36.0 + - - +
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Residues in contact with LYS 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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112B SER* 3.0 29.8 + - - +
113B GLU* 3.7 27.9 + - - +
114B GLY 3.3 0.2 - - - -
115B THR* 1.3 75.6 - - + +
117B ALA* 1.3 59.0 + - - +
119B THR* 3.1 7.9 + - - +
120B LYS* 2.9 32.6 + - - +
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Residues in contact with ALA 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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21A ALA* 3.8 19.0 - - - +
23A LEU* 4.3 7.6 - - + -
49A VAL* 3.8 16.6 - - + +
53A ALA* 3.5 28.5 - - + -
113B GLU 3.1 2.3 + - - +
114B GLY 3.1 9.9 + - - +
116B LYS* 1.3 81.0 - - - +
118B VAL* 1.3 57.1 + - - +
120B LYS* 3.8 0.9 - - - +
121B TYR* 2.8 31.4 + - - +
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Residues in contact with VAL 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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46A GLY* 4.0 23.1 - - - +
49A VAL* 4.0 19.3 - - + -
50A TYR* 4.0 17.9 - - + +
91B SER* 4.6 10.5 - - - +
114B GLY 3.1 13.7 + - - +
115B THR* 3.8 7.9 - - - +
117B ALA* 1.3 75.1 - - - +
119B THR* 1.3 56.4 + - - +
121B TYR* 3.7 4.1 - - + +
122B THR* 2.6 47.5 + - - +
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Residues in contact with THR 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 THR* 2.9 28.8 + - - +
116B LYS* 3.4 7.9 - - - +
118B VAL* 1.3 78.5 - - - +
120B LYS* 1.3 63.7 + - + +
122B THR* 3.6 5.3 - - - -
123B SER* 3.0 23.9 + - - -
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Residues in contact with LYS 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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15A LYS* 5.4 4.9 - - - +
19A SER 4.0 5.6 + - - -
20A ARG 3.5 10.3 + - - +
21A ALA 3.5 13.2 - - - +
22A GLY* 3.1 31.6 - - - +
116B LYS 2.9 15.7 + - - +
117B ALA 3.9 2.2 - - - +
119B THR* 1.3 79.0 - - - +
121B TYR* 1.3 54.6 + - - +
123B SER* 2.9 7.2 + - - +
124B SER* 2.7 45.9 + - - +
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Residues in contact with TYR 121 (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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17A ARG* 3.0 67.6 + - + -
20A ARG* 3.3 55.5 + - + -
21A ALA* 3.8 11.0 - - + -
45A ALA* 4.8 9.6 - - + +
46A GLY* 5.9 2.5 - - - -
49A VAL* 4.0 18.6 - - + -
117B ALA 2.8 19.6 + - - +
118B VAL* 3.8 5.8 - - + +
120B LYS* 1.3 77.1 - - - +
122B THR* 1.3 69.0 + - - +
124B SER 3.3 18.2 - - - +
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Residues in contact with THR 122 (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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118B VAL* 2.6 36.2 + - - +
119B THR* 3.6 6.2 - - - -
121B TYR* 1.3 83.7 - - - +
123B SER* 1.3 65.1 + - - +
124B SER 4.8 0.3 - - - -
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Residues in contact with SER 123 (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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119B THR* 3.0 15.2 + - - -
120B LYS* 2.9 16.5 + - - +
122B THR* 1.3 81.6 - - - +
124B SER* 1.3 73.1 + - - +
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Residues in contact with SER 124 (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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15A LYS* 5.0 9.1 + - - -
20A ARG* 2.8 55.7 + - - +
120B LYS* 2.7 33.1 + - - +
121B TYR 3.3 12.9 - - - +
122B THR 4.8 0.7 - - - -
123B SER* 1.3 83.9 + - - +
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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