Contacts of the strand formed by residues 87 - 94 (chain E) in PDB entry 3HG1
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 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E ARG* 4.6 2.7 - - - -
38E GLN 3.7 8.7 - - - -
39E ALA* 4.4 8.3 - - - -
85E ASP 3.5 1.3 + - - -
86E SER* 1.3 76.0 - - - +
88E PHE* 1.3 59.4 + - - -
89E TYR* 3.5 14.9 - - - -
110E ARG* 4.8 1.1 - - - -
111E LEU 2.9 31.0 + - - -
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Residues in contact with PHE 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 4.1 8.3 - - - -
41D GLY 3.8 14.4 - - - -
43D SER* 4.3 5.4 - - - -
37E ARG* 3.5 0.7 - - - -
38E GLN* 2.7 71.4 + - + +
87E GLY* 1.3 70.5 - - - -
89E TYR* 1.3 59.5 + - - +
90E LEU* 3.4 35.0 + - + +
107E GLU 3.8 12.6 - - - -
108E GLY 3.8 2.5 - - - -
109E SER 3.6 20.9 - - - -
110E ARG* 3.1 63.2 - - + +
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Residues in contact with TYR 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6E GLN* 2.6 24.1 - - - +
19E LEU* 5.1 2.0 - - + +
21E LEU* 3.9 23.6 - - + -
35E TRP* 4.8 2.2 - - + -
36E TYR 3.7 4.7 - - - +
37E ARG* 3.6 35.7 + - + -
47E LEU* 3.7 4.0 - - + -
64E LEU* 3.5 32.4 - - + +
76E LEU* 3.6 18.4 - - + -
85E ASP* 2.3 42.9 + - - +
87E GLY 3.5 18.4 - - - -
88E PHE* 1.3 70.8 - - - +
90E LEU* 1.3 54.8 - - - +
109E SER* 2.8 35.7 + - - +
111E LEU* 3.9 19.0 - - + +
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Residues in contact with LEU 90 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D SER* 3.5 17.0 - - - -
44D PRO* 3.5 24.7 - - + -
6E GLN* 3.6 2.2 - - - +
34E TYR 3.7 0.3 - - - +
35E TRP* 3.6 3.9 - - - -
36E TYR* 2.8 42.0 + - + +
38E GLN* 4.4 4.9 - - - +
44E LEU* 3.4 31.6 - - + -
88E PHE* 3.4 33.6 + - + +
89E TYR* 1.3 73.9 - - - +
91E CYS* 1.3 60.7 + - - +
92E ALA 4.1 0.3 + - - -
105E PHE* 4.1 13.2 - - + -
106E GLY 3.9 3.8 - - - +
108E GLY* 3.3 27.8 - - - -
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Residues in contact with CYS 91 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 4.0 5.1 - - + +
6E GLN* 3.3 16.5 + - - +
23E CYS* 2.1 50.3 - - + -
33E LEU* 5.4 3.1 - - - -
34E TYR 3.4 5.4 - - - -
35E TRP* 3.4 18.4 - - + -
74E PHE* 4.0 19.7 - - - -
90E LEU* 1.3 72.0 - - - +
92E ALA* 1.3 67.2 + - - +
105E PHE* 3.3 2.8 - - - -
106E GLY* 3.0 26.0 + - - -
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Residues in contact with ALA 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4E ILE* 5.0 1.3 - - - -
33E LEU* 3.4 3.5 - - - +
34E TYR* 2.8 39.3 + - + +
36E TYR* 5.0 1.6 - - + -
90E LEU 4.1 0.2 + - - -
91E CYS* 1.3 80.6 - - - +
93E TRP* 1.3 62.1 + - - +
103E LEU* 3.9 16.2 - - + -
104E PHE 3.0 17.0 - - - +
105E PHE* 3.4 28.3 - - + -
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Residues in contact with TRP 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E THR* 3.5 28.9 + - + +
4E ILE* 4.2 12.6 - - + -
25E VAL* 3.6 19.5 - - + +
28E THR* 3.3 37.2 - - + -
31E PRO* 3.9 8.7 - - + -
32E ASN 2.8 12.1 - - - +
33E LEU* 4.0 15.5 - - + -
34E TYR* 4.4 1.3 - - - -
92E ALA* 1.3 77.0 - - - +
94E SER* 1.3 84.9 + - - +
95E GLU* 3.3 37.0 - - + -
103E LEU* 3.1 5.1 - - - -
104E PHE* 2.7 81.5 + + + +
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Residues in contact with SER 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E PRO 3.6 0.2 - - - -
32E ASN* 2.7 55.8 + - - +
34E TYR* 3.1 18.2 + - - -
93E TRP* 1.3 82.5 - - - +
95E GLU* 1.3 62.0 + - - +
96E THR 3.4 0.2 + - - -
101E GLY* 5.2 5.4 - - - -
102E GLU 3.6 25.1 - - - -
103E LEU* 4.4 1.8 - - - -
104E PHE* 4.8 0.2 - - - -
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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