Contacts of the helix formed by residues 108 - 126 (chain A) in PDB entry 1W6T
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 ALA 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.4 31.9 - - + -
49A VAL 2.8 25.8 + - - +
50A GLU* 4.2 1.1 - - + +
103A LYS* 3.2 18.8 + - + -
107A GLY* 1.3 72.7 - - - -
109A ASN* 1.3 56.3 + - - +
111A ILE* 3.9 1.1 - - - +
112A LEU* 2.9 32.7 + - - +
345A ASN* 4.2 13.2 - - - +
348A GLY* 4.1 4.0 - - - +
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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
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20A THR* 5.4 2.4 + - - +
21A LEU* 3.7 13.0 - - + +
37A VAL* 3.5 31.2 - - + +
38A PRO 5.7 0.2 - - - +
50A GLU* 4.0 19.0 + - + +
51A LEU 2.9 44.7 + - - +
52A ARG* 5.5 1.0 - - - +
64A THR* 4.0 15.2 - - - +
67A ALA* 3.7 15.2 - - - +
107A GLY* 3.5 7.4 - - - -
108A ALA* 1.3 71.0 - - - +
110A ALA* 1.3 66.6 + - - -
113A GLY 3.0 18.9 + - - -
345A ASN* 6.1 0.7 - - - -
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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
----------------------------------------------------------
21A LEU* 3.9 5.8 - - - +
67A ALA* 3.6 12.8 - - + +
70A ASN* 4.5 1.1 - - + -
71A VAL* 3.6 26.4 - - + +
75A ILE* 4.0 11.2 - - + -
106A LEU 3.5 24.9 - - - +
107A GLY 3.1 2.6 + - - +
109A ASN* 1.3 81.5 + - - +
111A ILE* 1.3 63.1 + - - +
113A GLY* 3.4 0.9 + - - -
114A VAL* 3.3 27.9 + - - +
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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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75A ILE* 4.4 3.6 - - + -
94A MET* 3.4 40.0 - - + +
95A ILE* 4.9 0.9 - - - +
98A ASP* 4.0 21.8 - - + -
103A LYS* 3.8 34.5 - - + -
106A LEU* 4.2 18.2 - - + -
107A GLY 3.0 12.5 + - - +
108A ALA* 3.9 5.2 - - - +
110A ALA* 1.3 77.7 - - - +
112A LEU* 1.3 57.4 + - - +
114A VAL* 3.3 2.3 + - - +
115A SER* 2.9 23.2 + - - -
348A GLY 3.4 15.7 - - - +
349A THR* 3.6 18.6 - - + -
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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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37A VAL* 4.3 5.4 - - + -
38A PRO* 4.5 8.3 - - + -
108A ALA 2.9 19.7 + - - +
109A ASN* 4.2 2.5 - - - +
111A ILE* 1.3 76.7 - - - +
113A GLY* 1.3 64.3 + - - +
115A SER* 3.1 2.0 + - - -
116A ILE* 2.9 46.0 + - + +
344A VAL* 3.8 26.2 - - + +
345A ASN* 3.6 34.5 - - + -
348A GLY* 3.1 26.0 + - - +
349A THR* 4.1 13.5 - - - +
350A LEU* 4.3 3.1 - - + +
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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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21A LEU* 4.4 0.2 - - - -
23A VAL* 3.5 22.1 - - - +
35A GLY* 3.9 10.8 - - - +
37A VAL* 3.4 19.4 - - - +
109A ASN 3.0 12.7 + - - -
110A ALA 3.4 0.2 + - - -
111A ILE 3.2 0.2 - - - -
112A LEU* 1.3 76.2 - - - +
114A VAL* 1.3 56.6 + - - +
116A ILE* 3.6 0.8 + - - -
117A ALA* 3.0 31.0 + - - +
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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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7A VAL* 4.0 12.6 - - + -
23A VAL* 3.7 13.0 - - + +
25A VAL* 5.1 0.7 - - + -
71A VAL* 3.8 28.3 - - + -
75A ILE* 4.0 17.9 - - + -
79A ILE* 4.7 8.7 - - + -
90A ILE* 4.9 0.4 - - + -
94A MET* 3.5 26.7 - - + -
110A ALA 3.3 14.4 + - - +
111A ILE 3.6 1.1 - - - +
112A LEU 3.2 0.2 - - - -
113A GLY* 1.3 73.5 - - - +
115A SER* 1.3 64.8 + - - +
117A ALA* 3.2 0.4 + - - -
118A VAL* 2.8 43.6 + - + +
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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* 3.0 23.8 + - - +
90A ILE* 5.8 0.4 - - - -
91A ASP* 2.6 28.9 + - - -
94A MET* 3.7 4.9 - - - +
111A ILE 2.9 14.9 + - - -
112A LEU* 3.1 14.8 + - - -
114A VAL* 1.3 75.3 - - - +
116A ILE* 1.3 63.0 + - - +
118A VAL* 3.6 2.9 + - - +
119A ALA 3.2 12.3 + - - -
349A THR* 4.1 3.4 - - - -
350A LEU* 2.9 30.7 + - - +
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Residues in contact with ILE 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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35A GLY* 3.8 11.7 - - - -
36A MET 4.1 16.8 - - - +
37A VAL* 5.3 0.7 - - + -
38A PRO* 5.8 0.9 - - + -
112A LEU* 2.9 48.2 + - + +
113A GLY 4.0 3.4 - - - +
115A SER* 1.3 73.2 - - - +
117A ALA* 1.3 67.6 + - - +
119A ALA* 3.2 2.9 + - - +
120A ARG* 2.9 43.8 + - + +
344A VAL* 4.9 8.1 - - + -
350A LEU* 4.0 18.2 - - + -
378A ASP* 4.6 2.5 - - - +
380A THR* 3.6 28.7 - - + +
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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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23A VAL* 3.4 27.6 - - + +
25A VAL* 3.5 21.4 - - + +
33A GLY* 3.5 10.1 - - - +
34A ARG 4.2 3.1 - - - -
35A GLY* 3.6 9.8 - - - +
113A GLY 3.0 19.5 + - - +
114A VAL 3.8 1.1 - - - +
116A ILE* 1.3 76.4 - - - +
118A VAL* 1.3 58.0 + - - +
120A ARG* 3.4 0.6 + - - -
121A ALA* 2.8 30.0 + - - +
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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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4A ILE* 4.1 15.3 - - + -
25A VAL* 4.0 21.3 - - + -
79A ILE* 4.7 1.8 - - + -
84A VAL* 3.3 24.5 - - + +
87A GLN* 3.4 15.9 - - - +
90A ILE* 3.7 26.9 - - + -
114A VAL* 2.8 33.8 + - + +
115A SER* 3.8 4.9 - - - +
117A ALA* 1.3 72.9 - - - +
119A ALA* 1.3 59.4 + - - +
121A ALA* 3.2 2.9 + - - +
122A ALA* 2.8 28.8 + - - +
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Residues in contact with ALA 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* 3.3 17.8 + - - +
115A SER 3.2 2.8 + - - -
116A ILE 3.2 5.2 + - - +
118A VAL* 1.3 77.7 - - - +
120A ARG* 1.3 58.9 + - + +
122A ALA* 3.2 3.3 + - - +
123A ALA* 3.0 28.1 + - - +
130A LEU* 4.1 6.3 - - + -
133A TYR* 3.7 12.4 - - + -
134A LEU* 4.0 17.7 - - + -
350A LEU* 3.5 27.8 - - + -
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Residues in contact with ARG 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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32A PHE 3.9 0.6 - - - +
33A GLY* 3.9 13.5 - - - -
34A ARG 3.2 26.4 + - - +
116A ILE* 2.9 35.1 + - + +
117A ALA 3.8 3.6 - - - +
119A ALA* 1.3 74.8 - - + +
121A ALA* 1.4 58.3 + - - +
123A ALA* 3.4 3.7 + - - +
124A ASP* 2.9 28.9 + - - +
130A LEU* 3.4 37.4 - - + +
378A ASP* 3.9 7.6 + - - -
379A SER* 4.8 6.7 + - - +
380A THR* 3.0 26.3 + - - +
383A ASP* 5.0 2.6 + - - -
409A GLN* 5.9 2.2 - - - +
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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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25A VAL* 3.7 24.2 - - + +
27A THR* 4.8 2.5 - - + -
31A ALA* 3.8 5.8 - - - +
32A PHE* 3.7 15.5 - - - +
33A GLY* 3.5 13.4 - - - +
84A VAL* 3.7 9.6 - - + +
117A ALA 2.8 18.9 + - - +
118A VAL 3.6 4.0 - - - +
120A ARG* 1.4 75.1 - - - +
122A ALA* 1.3 58.1 + - - +
124A ASP* 3.3 2.6 + - - +
125A TYR* 2.8 29.3 + - - +
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Residues in contact with ALA 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* 3.6 31.8 - - + +
85A ARG* 4.2 3.1 - - + -
118A VAL 2.8 20.0 + - - +
119A ALA* 3.2 2.2 + - - +
121A ALA* 1.3 72.1 - - - +
123A ALA* 1.3 59.7 + - - +
125A TYR* 3.2 2.3 + - - +
126A LEU* 2.9 32.4 + - - +
133A TYR* 3.4 33.0 - - + +
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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 ALA 3.0 13.4 + - - +
120A ARG* 3.6 8.1 - - - +
122A ALA* 1.3 74.8 - - - +
124A ASP* 1.3 58.7 + - - +
126A LEU* 3.3 0.9 + - - -
127A GLU* 2.8 25.3 + - - -
128A ILE* 3.1 29.7 + - - +
130A LEU* 4.0 18.8 - - + +
133A TYR* 3.8 24.5 - - + -
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Residues in contact with ASP 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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30A GLY 4.5 0.9 - - - +
31A ALA* 3.2 9.8 - - - +
32A PHE* 2.8 46.6 + - - +
120A ARG 2.9 11.5 + - - +
121A ALA 3.5 3.8 - - - +
123A ALA* 1.3 76.7 - - - +
125A TYR* 1.3 63.1 + - - +
127A GLU* 3.1 19.6 + - - +
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Residues in contact with TYR 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* 3.7 23.8 - - + +
2A SER* 3.6 30.3 + - - -
27A THR* 4.3 1.1 - - - -
29A SER* 3.4 28.7 - - - -
31A ALA* 3.6 11.8 - - + +
84A VAL* 4.1 8.7 - - + -
85A ARG* 4.2 17.7 + - - -
121A ALA 2.8 20.4 + - - +
122A ALA* 3.2 8.9 + - - +
124A ASP* 1.3 74.2 - - - +
126A LEU* 1.3 83.3 + - + +
127A GLU* 3.4 8.0 + - - +
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Residues in contact with LEU 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 ARG* 3.9 26.5 - - - +
122A ALA 2.9 13.4 + - - +
125A TYR* 1.3 96.1 - - + +
127A GLU* 1.3 68.5 + - - +
128A ILE* 3.5 26.9 + - + +
133A TYR* 3.8 34.5 - - + -
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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
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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