Contacts of the helix formed by residues 107 - 126 (chain A) in PDB entry 2XSX
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 GLY 107 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 3.7 7.4 - - - -
49A LEU* 3.9 11.2 - - - +
103A LYS* 2.8 16.6 + - - -
104A SER* 4.2 3.2 - - - -
105A LYS 3.6 1.4 - - - -
106A PHE* 1.3 80.2 - - - +
108A ALA* 1.3 65.5 + - - -
109A ASN* 3.1 12.3 - - - -
110A ALA 3.1 2.1 + - - -
111A ILE* 3.1 24.1 + - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ALA* 3.5 32.8 - - + +
47A LEU 2.8 24.4 + - - +
48A GLU* 4.2 2.0 - - - +
103A LYS* 3.3 18.3 + - + -
107A GLY* 1.3 72.8 - - - -
109A ASN* 1.3 56.6 + - - +
111A ILE* 4.0 0.2 - - - -
112A LEU* 2.9 33.1 + - - +
345A ASN* 4.4 10.7 - - - +
348A GLY* 4.1 4.4 - - - +
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Residues in contact with ASN 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A THR* 5.6 2.1 + - - +
20A VAL* 4.0 16.3 - - + +
35A VAL* 3.4 32.6 - - + +
48A GLU* 3.9 18.2 - - + +
49A LEU* 2.9 46.6 + - - +
50A ARG* 5.2 1.0 - - - +
62A VAL* 3.9 17.6 - - - +
65A ALA* 3.9 9.2 - - - +
107A GLY* 3.7 6.9 - - - -
108A ALA* 1.3 73.0 - - - +
110A ALA* 1.3 64.8 + - - -
113A GLY* 3.2 17.3 + - - -
345A ASN* 6.5 0.2 - - - -
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Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A VAL* 4.9 0.7 - - - -
65A ALA* 3.7 24.0 - - + +
68A ASN* 4.8 1.6 - - + -
69A ILE* 3.6 20.6 - - + +
73A LEU* 4.3 3.1 - - + -
106A PHE* 3.3 32.3 - - + +
107A GLY 3.1 2.8 + - - +
109A ASN* 1.3 78.4 + - - +
111A ILE* 1.3 67.9 + - - +
113A GLY 3.4 1.6 + - - -
114A VAL* 3.4 24.8 + - - +
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Residues in contact with ILE 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A LEU* 4.1 20.4 - - + -
91A ASP 5.7 0.4 - - - +
94A MET* 3.6 38.8 - - + +
95A ILE* 5.1 3.6 - - + -
98A ASP* 3.8 31.6 - - + +
103A LYS* 3.9 35.4 - - + -
106A PHE* 4.3 6.5 - - + -
107A GLY 3.1 11.3 + - - +
108A ALA 4.1 1.6 - - - +
110A ALA* 1.3 77.7 - - - +
112A LEU* 1.3 62.9 + - - +
114A VAL* 3.3 0.9 + - - -
115A SER* 2.9 19.4 + - - -
348A GLY 3.6 16.4 - - - +
349A SER* 4.9 5.2 - - - -
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Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A VAL* 4.2 14.1 - - + -
36A PRO* 4.6 2.7 - - + -
108A ALA 2.9 19.7 + - - +
109A ASN* 4.3 2.5 - - - +
110A ALA 3.4 0.2 - - - -
111A ILE* 1.3 77.9 - - - +
113A GLY* 1.3 64.0 + - - +
115A SER* 3.1 3.2 + - - -
116A LEU* 2.9 50.5 + - + +
344A VAL* 4.1 16.6 - - + +
345A ASN* 3.5 38.6 - - + +
348A GLY* 3.4 26.3 + - - +
349A SER* 3.9 15.5 - - - +
350A VAL* 4.3 1.3 - - + +
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 3.6 24.4 - - - +
33A ALA* 4.3 5.8 - - - +
35A VAL* 3.6 18.8 - - - +
109A ASN 3.2 12.4 + - - -
110A ALA 4.0 0.4 - - - -
111A ILE 3.3 0.4 - - - -
112A LEU* 1.3 77.4 - - - +
114A VAL* 1.3 62.1 + - - +
116A LEU* 3.6 5.6 + - - +
117A ALA* 3.2 23.4 + - - +
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A ILE* 4.6 12.6 - - + -
22A VAL* 4.4 11.7 - - + -
24A LEU* 5.5 1.3 - - + -
69A ILE* 4.1 28.9 - - + -
73A LEU* 4.3 11.2 - - + -
74A GLY* 5.8 1.8 - - - +
77A LEU* 3.6 30.7 - - + -
94A MET* 3.7 13.7 - - - -
110A ALA 3.4 13.1 + - - +
111A ILE 3.3 6.2 + - - +
112A LEU 3.2 0.4 - - - -
113A GLY* 1.3 73.0 - - - +
115A SER* 1.3 67.8 + - - +
117A ALA* 3.2 2.5 + - - +
118A VAL* 2.9 28.9 + - + +
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Residues in contact with SER 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLN* 3.1 25.1 + - - +
91A ASP* 2.6 25.9 + - - -
94A MET* 3.7 9.1 - - - +
111A ILE 2.9 14.7 + - - -
112A LEU* 3.1 12.8 + - - -
114A VAL* 1.3 76.7 - - - +
116A LEU* 1.3 59.7 + - - +
118A VAL* 3.6 2.8 + - - +
119A CYS* 3.2 13.5 + - - +
349A SER* 4.2 4.5 - - - -
350A VAL* 2.9 28.2 + - - +
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Residues in contact with LEU 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ALA* 3.5 21.8 - - + -
34A ALA 3.8 24.5 - - - +
35A VAL* 4.6 2.7 - - + -
36A PRO* 5.4 2.0 - - + -
112A LEU* 2.9 48.4 + - + +
113A GLY* 3.9 1.3 - - - +
115A SER* 1.3 72.6 - - - +
117A ALA* 1.3 65.5 + - - +
119A CYS* 3.3 4.9 + - - +
120A LYS* 3.1 26.5 + - - +
344A VAL* 5.2 7.2 - - + -
350A VAL* 3.9 12.8 - - + -
378A ASP* 5.2 3.1 - - - +
380A PHE* 3.7 45.2 - - + -
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Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.1 18.2 - - + +
24A LEU* 3.9 17.0 - - + +
31A PHE* 3.8 24.5 - - - +
33A ALA* 4.3 7.6 - - + -
113A GLY 3.2 14.8 + - - +
114A VAL 3.2 4.1 + - - +
116A LEU* 1.3 79.9 - - - +
118A VAL* 1.3 62.0 + - - +
120A LYS* 3.3 7.8 + - - +
121A ALA* 3.1 23.6 + - - +
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A MET* 4.2 9.2 - - + -
24A LEU* 3.6 24.2 - - + -
77A LEU* 4.4 1.1 - - + -
84A VAL* 3.5 28.2 - - + +
87A GLN* 3.7 13.9 - - - +
90A VAL* 4.1 34.1 - - + -
114A VAL* 2.9 33.6 + - + +
115A SER* 3.7 5.2 - - - +
117A ALA* 1.3 76.6 - - - +
119A CYS* 1.3 56.8 + - - +
121A ALA 3.3 0.7 + - - -
122A GLY 2.8 25.1 + - - -
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Residues in contact with CYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLN* 3.1 20.8 + - - +
115A SER 3.2 11.6 + - - +
116A LEU 3.3 8.3 + - - +
118A VAL* 1.3 75.3 - - - +
120A LYS* 1.3 63.4 + - - +
122A GLY 3.3 0.3 + - - -
123A ALA* 3.1 20.8 + - - +
130A LEU* 3.9 15.3 - - - +
133A HIS* 3.3 29.2 - - - -
134A ILE* 4.1 13.5 - - - -
137A LEU* 4.2 4.0 - - - -
350A VAL* 4.2 12.3 - - + -
380A PHE* 4.1 17.9 - - + -
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Residues in contact with LYS 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A PHE* 3.7 24.2 - - + -
32A ARG 2.9 34.9 + - - +
33A ALA* 3.9 8.7 - - + +
116A LEU 3.1 16.1 + - - +
117A ALA* 3.3 7.6 + - - +
119A CYS* 1.3 79.6 - - - +
121A ALA* 1.3 60.8 + - - +
123A ALA* 3.5 4.7 + - - +
124A ALA* 3.5 14.9 + - - +
130A LEU* 4.0 30.2 - - + +
378A ASP* 3.1 25.0 + - - -
379A THR* 4.9 3.2 + - - +
380A PHE* 3.9 25.9 - - + +
511A EDO 4.0 7.1 + - - -
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Residues in contact with ALA 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A LEU* 3.4 32.3 - - + -
26A THR* 4.0 7.7 + - + -
28A LYS* 5.8 0.3 - - - +
31A PHE* 3.7 23.4 - - + -
84A VAL* 3.4 17.5 - - + +
117A ALA 3.1 11.0 + - - +
120A LYS* 1.3 76.0 - - - +
122A GLY* 1.3 62.5 + - - +
124A ALA* 3.3 4.3 + - - +
125A GLU* 3.1 22.3 + - - +
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Residues in contact with GLY 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A VAL* 3.5 33.4 - - - +
85A ALA* 4.0 3.5 - - - +
118A VAL 2.8 12.5 + - - -
119A CYS 3.3 2.2 + - - -
121A ALA* 1.3 73.6 - - - +
123A ALA* 1.3 67.0 + - - +
125A GLU* 3.3 2.3 + - - +
126A LYS* 3.1 28.9 + - - +
133A HIS* 4.0 8.5 - - - -
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Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A CYS 3.1 9.9 + - - +
120A LYS 3.7 9.9 - - - +
121A ALA 3.3 0.2 - - - -
122A GLY* 1.3 75.4 - - - +
124A ALA* 1.3 62.0 + - - +
126A LYS* 3.2 4.5 + - - +
127A GLY 3.2 4.2 + - - -
128A VAL* 3.0 40.0 + - - +
130A LEU* 3.7 20.9 - - + +
133A HIS* 3.5 30.7 - - + -
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LYS* 3.9 24.8 - - + +
31A PHE* 3.5 37.5 - - + -
120A LYS 3.5 1.8 + - - +
121A ALA 3.3 4.4 + - - +
122A GLY 3.3 0.4 - - - -
123A ALA* 1.3 80.4 - - - +
125A GLU* 1.4 55.9 + - - +
127A GLY* 3.1 18.6 + - - +
128A VAL 4.5 2.7 - - - -
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Residues in contact with GLU 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.1 50.3 - - - +
28A LYS* 4.4 18.5 - - + +
83A SER* 3.1 15.9 + - - -
84A VAL* 3.8 8.5 - - + -
85A ALA* 3.6 17.4 + - - +
121A ALA 3.1 13.4 + - - +
122A GLY 3.3 8.0 + - - +
124A ALA* 1.4 75.2 - - - +
126A LYS* 1.3 62.8 + - - +
127A GLY 3.6 0.5 + - - -
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Residues in contact with LYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ALA* 3.9 19.7 - - + +
122A GLY 3.1 14.0 + - - +
123A ALA 3.6 5.4 - - - +
124A ALA 3.2 0.2 - - - -
125A GLU* 1.3 80.4 - - - +
127A GLY* 1.3 60.3 + - - +
128A VAL* 3.6 16.5 + - + +
133A HIS* 2.8 42.1 + - + +
136A ASP* 2.9 37.5 + - - +
137A LEU* 5.3 1.8 - - - +
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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