Contacts of the helix formed by residues 99 - 120 (chain B) in PDB entry 3HSR
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 THR 99 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ASP* 2.6 41.7 + - - +
81B TYR 2.9 9.3 + - - -
82B VAL 3.8 10.8 - - - +
83B VAL* 3.1 35.2 - - + -
97B SER 3.9 0.2 + - - -
98B LEU* 1.3 75.0 - - - +
100B GLU* 1.3 61.6 + - - +
101B GLN* 3.3 3.3 + - - -
102B GLY 2.7 15.1 + - - -
103B LYS* 2.8 27.4 + - - +
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU 4.6 1.6 - - - +
99B THR* 1.3 75.8 - - - +
101B GLN* 1.3 63.7 + - - +
103B LYS* 3.2 36.6 + - - +
104B ALA* 2.9 25.7 + - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B LYS 3.9 8.8 + - - -
80B ASP* 2.9 33.4 - - - +
81B TYR* 3.6 32.0 + - + -
99B THR* 3.3 0.6 + - - -
100B GLU* 1.3 78.4 - - - +
102B GLY* 1.3 56.6 + - - +
104B ALA* 3.1 6.6 + - - +
105B ILE* 2.8 30.3 + - + +
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B LEU* 5.4 0.6 - - - +
81B TYR* 3.4 29.5 - - - +
98B LEU* 4.2 9.6 - - - +
99B THR* 2.7 15.2 + - - -
101B GLN* 1.3 74.1 - - - +
103B LYS* 1.3 61.1 + - - +
105B ILE* 3.2 25.7 - - - +
106B LYS* 3.3 14.0 + - - +
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Residues in contact with LYS 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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49B ASN* 3.1 65.7 + - + +
98B LEU* 3.7 22.8 - - + +
99B THR 2.8 18.8 + - - +
100B GLU* 3.2 37.3 + - - +
102B GLY* 1.3 72.7 - - - +
104B ALA* 1.3 62.2 + - - +
106B LYS* 3.6 13.5 + - - +
107B SER* 4.1 3.1 + - - -
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Residues in contact with ALA 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 GLU 2.9 18.8 + - - +
101B GLN* 3.1 7.2 + - - +
103B LYS* 1.3 76.1 - - - +
105B ILE* 1.3 64.7 + - - +
107B SER* 3.2 21.5 + - - -
108B PRO* 3.4 4.0 - - - +
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Residues in contact with ILE 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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34B TYR* 3.9 29.8 - - + -
36B LEU* 5.4 1.1 - - + -
44B LEU* 4.3 9.0 - - + -
81B TYR* 4.1 32.5 - - + +
101B GLN* 2.8 17.6 + - + +
102B GLY* 3.2 22.2 - - - +
104B ALA* 1.3 72.7 - - - +
106B LYS* 1.3 58.6 + - + +
107B SER 3.1 0.2 - - - -
108B PRO* 3.0 27.3 - - + +
109B LEU* 3.1 34.5 - - + +
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Residues in contact with LYS 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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44B LEU* 3.3 23.3 - - + +
45B MET* 4.0 34.6 + - + +
47B ILE 2.5 28.3 + - - -
48B GLU* 3.9 8.9 + - - +
49B ASN* 3.3 20.2 + - - +
98B LEU* 3.4 22.0 - - + -
102B GLY 3.3 10.3 + - - +
103B LYS 3.7 9.2 - - - +
104B ALA 3.2 0.6 - - - -
105B ILE* 1.3 78.5 - - + +
107B SER* 1.3 66.2 + - - +
109B LEU* 3.8 7.6 - - + -
110B ALA* 3.2 21.3 + - - +
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Residues in contact with SER 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 LYS 4.1 2.5 + - - -
104B ALA* 3.2 11.4 + - - -
105B ILE 3.1 0.2 - - - -
106B LYS* 1.3 79.4 - - - +
108B PRO* 1.3 72.4 - - - +
110B ALA* 3.4 14.5 + - - +
111B GLU* 3.8 11.3 + - - +
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Residues in contact with PRO 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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34B TYR* 3.3 28.7 + - + +
104B ALA 3.4 7.0 - - - +
105B ILE* 3.0 31.6 - - + +
107B SER* 1.3 95.5 - - - +
109B LEU* 1.3 63.3 + - - +
111B GLU* 3.1 35.5 + - - +
112B ILE* 3.8 7.5 + - - +
115B LYS* 5.7 0.5 + - - -
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Residues in contact with LEU 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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31B LEU* 3.8 16.8 - - + -
34B TYR* 4.0 16.2 - - + -
36B LEU* 3.8 22.2 - - + -
41B TYR* 3.6 18.6 + - + -
44B LEU* 4.1 9.2 - - + -
45B MET* 3.8 19.7 - - - -
105B ILE* 3.1 47.8 + - + +
106B LYS* 4.1 3.6 - - + +
107B SER 3.3 0.4 - - - -
108B PRO* 1.3 76.2 - - + +
110B ALA* 1.3 57.2 + - - +
112B ILE* 2.9 48.3 + - + +
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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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6A MET* 4.8 15.9 - - + +
41B TYR* 5.6 1.3 - - - -
45B MET* 4.1 18.7 - - + +
106B LYS 3.2 19.2 + - - +
107B SER* 3.4 8.1 - - - +
108B PRO 3.2 0.2 - - - -
109B LEU* 1.3 75.8 - - - +
111B GLU* 1.3 62.1 + - + +
112B ILE 3.1 0.9 + - - -
113B SER* 3.7 12.0 + - - -
114B VAL* 4.0 11.4 - - - +
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Residues in contact with GLU 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 SER* 3.9 9.1 + - - +
108B PRO* 3.1 28.1 + - - +
110B ALA* 1.3 77.9 - - + +
112B ILE* 1.3 56.8 + - + +
113B SER 3.5 0.2 - - - -
114B VAL* 3.3 11.4 + - + +
115B LYS* 3.0 55.6 + - - +
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Residues in contact with ILE 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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27B TYR* 3.6 29.4 - - + +
30B TYR* 4.0 31.9 - - + -
31B LEU* 3.5 29.2 - - + -
34B TYR* 4.2 13.2 - - + -
41B TYR* 4.5 3.4 - - + -
108B PRO 4.0 7.2 - - - +
109B LEU* 2.9 31.8 + - + +
111B GLU* 1.3 74.1 - - - +
113B SER* 1.3 61.8 + - - +
115B LYS* 3.1 13.9 + - + +
116B VAL* 2.9 31.9 + - + +
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Residues in contact with SER 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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6A MET* 6.6 0.2 - - - -
9A SER* 3.8 22.7 - - - +
10A LYS* 4.8 3.7 - - - -
13A CYS* 2.9 10.9 - - - +
27B TYR* 2.7 28.4 + - - -
41B TYR* 2.9 19.9 + - - -
109B LEU 4.3 0.2 + - - -
110B ALA 3.7 7.7 + - - -
111B GLU 3.5 0.4 - - - -
112B ILE* 1.3 77.3 - - - +
114B VAL* 1.3 62.7 + - - +
116B VAL* 3.4 1.9 + - - +
117B PHE* 3.0 25.3 + - - +
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Residues in contact with VAL 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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6A MET* 3.3 35.9 - - + -
9A SER* 3.6 17.3 - - - +
110B ALA 4.0 10.8 - - - +
111B GLU* 3.3 10.7 + - - +
112B ILE 3.2 0.6 - - - -
113B SER* 1.3 76.2 - - - +
115B LYS* 1.3 59.4 + - + +
117B PHE* 3.2 3.8 + - + +
118B ASN* 2.9 54.8 + - - +
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Residues in contact with LYS 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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30B TYR* 3.8 39.4 - - + +
34B TYR* 5.9 1.4 + - - -
108B PRO 5.7 0.6 + - - -
111B GLU* 3.0 45.0 + - + +
112B ILE* 3.4 14.6 - - + +
114B VAL* 1.3 75.4 - - + +
116B VAL* 1.3 66.0 + - - +
118B ASN* 3.6 7.0 + - - +
119B GLU* 3.2 26.9 + - - +
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Residues in contact with VAL 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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23B ILE* 4.8 3.4 - - + +
26B LYS* 4.1 16.2 - - + +
27B TYR* 4.1 36.3 - - + +
30B TYR* 4.0 24.5 - - + -
112B ILE* 2.9 23.7 + - + +
113B SER 3.8 3.8 - - - +
115B LYS* 1.3 76.3 - - - +
117B PHE* 1.3 64.4 + - - +
119B GLU* 3.1 17.2 + - - +
120B PHE* 3.2 39.6 + - + -
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Residues in contact with PHE 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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8A LEU* 4.4 24.5 - - + -
9A SER* 3.7 21.5 - - - -
12A LEU* 3.8 17.0 - - + -
113B SER 3.0 17.1 + - - +
114B VAL* 3.5 4.7 - - + +
116B VAL* 1.3 76.0 - - - +
118B ASN* 1.3 73.6 + - - +
119B GLU 3.1 4.9 + - - -
120B PHE* 3.2 24.4 + - - +
122B ILE* 3.6 31.9 - - + +
123B SER 4.6 5.6 - - - -
124B GLU* 4.6 11.9 - - + -
127B ALA* 3.8 27.4 - - + -
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Residues in contact with ASN 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 VAL* 2.9 41.7 + - - +
115B LYS* 3.9 7.0 - - - +
117B PHE* 1.3 88.6 - - - +
119B GLU* 1.3 58.0 + - - +
120B PHE 3.5 4.4 - - - +
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Residues in contact with GLU 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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26B LYS* 3.1 42.4 + - + +
30B TYR* 2.3 39.4 + - - -
115B LYS 3.2 13.2 + - - +
116B VAL* 3.1 7.6 + - - +
117B PHE 3.1 0.2 - - - -
118B ASN* 1.3 77.1 - - - +
120B PHE* 1.3 65.1 + - - +
121B ASN* 3.9 4.3 + - - +
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Residues in contact with PHE 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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137A PHE* 3.9 20.2 - + + -
141A ASN* 3.9 14.6 - - + -
142A PHE* 3.7 26.7 - + - -
22B GLU 4.1 11.7 - - - -
23B ILE* 4.0 23.6 - - + -
26B LYS* 3.5 35.9 - - + -
116B VAL* 3.2 40.2 + - + -
117B PHE* 3.2 17.9 + - - +
118B ASN 4.2 4.0 - - - +
119B GLU* 1.3 83.7 - - - +
121B ASN* 1.3 61.6 + - - +
122B ILE* 3.1 21.3 + - + +
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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
------------------------------------------------------------
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