Contacts of the strand formed by residues 106 - 113 (chain B) in PDB entry 1HWG
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 106 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A LEU* 3.8 42.6 - - + +
51A SER* 4.2 7.9 - - - +
164A TYR* 4.2 7.4 - - - +
168A LYS* 5.0 1.8 - - - +
70B ARG* 3.3 2.9 - - - -
71B ARG* 2.9 66.0 + - + -
76B TRP* 3.8 10.9 - - + -
104B TRP 4.2 4.5 - - - +
105B ILE* 1.4 83.4 - - + +
107B TYR* 1.3 59.7 + - - +
108B CYS* 6.0 0.2 - - - -
122B CYS* 6.2 0.2 - - + -
123B PHE 3.5 7.6 - - - +
124B SER* 4.4 2.7 - - - +
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Residues in contact with TYR 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PHE* 3.7 22.7 - + - -
68B TYR* 4.5 18.6 - + + -
69B THR 3.3 7.6 - - - -
70B ARG* 3.8 32.8 + - + -
96B PHE* 5.0 1.8 - + - -
100B PHE 2.6 30.6 + - - -
101B THR* 3.2 0.3 - - - -
102B SER* 3.0 38.7 + - - -
105B ILE* 3.5 21.8 - - + -
106B PRO* 1.3 75.6 - - - +
108B CYS* 1.3 63.0 + - - +
109B ILE* 5.6 1.1 - - + -
121B LYS 3.9 0.3 - - - +
122B CYS* 3.2 6.1 - - - +
123B PHE* 2.8 55.8 + + + +
125B VAL* 3.7 13.7 - - + -
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Residues in contact with CYS 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LEU* 5.4 0.7 - - - -
46A GLN* 3.9 19.1 - - - +
68B TYR* 3.3 4.2 - - - +
69B THR* 2.8 49.3 + - + +
76B TRP* 3.8 22.4 - - + -
77B THR* 6.5 0.2 - - + -
80B TRP* 3.6 13.6 - - + -
106B PRO* 6.0 0.4 - - - -
107B TYR* 1.3 73.6 - - - +
109B ILE* 1.3 62.1 + - - +
120B GLU* 4.6 2.9 - - - +
121B LYS 3.3 2.7 - - - -
122B CYS* 2.3 41.5 - - - -
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Residues in contact with ILE 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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35B PHE* 3.6 27.1 - - + -
38B CYS* 5.3 1.3 - - - -
46B PHE* 4.8 1.3 - - + -
48B CYS* 3.9 26.5 - - - -
66B LEU* 3.7 17.0 - - + -
67B PHE 3.4 2.5 - - - -
68B TYR* 3.6 20.0 - - + -
80B TRP* 4.1 1.8 - - - -
96B PHE* 3.9 23.1 - - + -
107B TYR* 5.6 1.8 - - + -
108B CYS* 1.3 73.3 - - - +
110B LYS* 1.3 60.3 + - - +
120B GLU* 3.1 4.4 - - - +
121B LYS* 2.8 46.4 + - + +
123B PHE* 3.9 21.3 - - + -
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Residues in contact with LYS 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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35B PHE* 4.0 5.4 - - - -
65B GLN 4.0 0.2 - - - +
66B LEU* 3.5 3.5 - - - +
67B PHE* 2.8 60.2 + - + +
80B TRP* 3.7 41.9 - - + +
109B ILE* 1.3 75.6 - - - +
111B LEU* 1.3 59.5 + - - +
112B THR* 4.2 5.5 + - + -
117B THR* 3.7 27.3 + - + +
119B ASP 3.2 12.1 - - - +
120B GLU* 4.2 11.0 - - + -
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Residues in contact with LEU 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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33B PRO* 3.6 43.5 - - + +
34B LYS* 4.3 5.2 - - - +
35B PHE* 3.5 26.6 - - + -
50B TRP* 3.6 44.6 - - + -
64B ILE* 3.7 13.7 - - + -
65B GLN 3.3 13.5 - - - +
66B LEU* 4.2 1.6 - - + -
110B LYS* 1.3 72.5 - - - +
112B THR* 1.3 61.6 + - - +
117B THR* 3.6 2.9 - - - -
118B VAL* 2.9 27.6 + - + +
119B ASP* 2.7 17.7 + - + +
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Residues in contact with THR 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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63B PRO 3.4 0.5 - - - +
64B ILE* 3.0 10.8 - - - +
65B GLN* 3.0 39.6 + - - +
67B PHE* 3.6 37.2 - - + -
110B LYS* 4.5 9.0 - - + +
111B LEU* 1.3 79.6 - - - +
113B SER* 1.3 60.2 + - - +
114B ASN 3.9 0.2 - - - -
115B GLY* 3.8 21.0 + - - +
116B GLY 3.1 8.1 - - - -
117B THR* 3.9 18.4 - - - +
118B VAL* 4.4 1.8 - - - -
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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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32B GLU* 4.6 4.8 + - - -
33B PRO* 4.3 18.5 - - - +
63B PRO 3.5 4.4 - - - -
64B ILE* 4.3 10.2 - - - +
112B THR* 1.3 70.9 - - - +
114B ASN* 1.3 75.1 + - - +
116B GLY* 2.7 20.4 + - - +
118B VAL* 3.8 23.7 - - - +
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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