Contacts of the strand formed by residues 6 - 14 (chain A) in PDB entry 4EFG
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 6 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A GLN 3.4 1.0 + - - -
5A ASN* 1.3 74.7 - - - +
7A THR* 1.3 63.0 + - - -
8A TRP* 3.3 12.5 - - - -
41A VAL* 3.5 3.6 - - - +
42A ILE 2.9 33.3 + - - +
132A LYS* 4.3 8.3 - - - -
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Residues in contact with THR 7 (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 GLY* 1.3 74.6 - - - -
8A TRP* 1.3 62.9 + - - +
9A GLU* 3.9 11.0 - - - +
39A THR* 3.7 23.8 - - + -
40A LEU 3.5 3.1 - - - -
41A VAL* 4.0 18.0 - - + +
132A LYS* 3.6 7.4 - - - +
133A LYS* 2.8 40.0 + - + -
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Residues in contact with TRP 8 (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 ASP 4.7 2.0 - - - -
4A GLN* 3.0 31.0 + - - -
5A ASN 4.3 0.2 - - - -
6A GLY 3.3 20.1 + - - -
7A THR* 1.3 75.7 - - - +
9A GLU* 1.3 63.4 - - - +
39A THR* 3.3 5.0 - - - -
40A LEU* 2.7 50.4 + - + +
42A ILE* 4.1 15.5 - - + -
110A ILE* 3.6 30.1 - - + -
112A GLY 5.4 0.9 - - - -
113A ASP* 3.6 16.6 - - - -
114A LYS 3.9 1.1 - - - -
115A LEU* 3.5 32.6 - - + +
130A PHE* 3.6 17.0 - - + -
131A LYS 3.5 5.4 - - - -
132A LYS* 3.4 57.0 - - + -
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Residues in contact with GLU 9 (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 THR* 3.7 7.0 - - - +
8A TRP* 1.3 80.6 + - - +
10A MET* 1.3 67.0 + - - +
11A GLU* 3.5 3.3 + - - +
37A THR* 5.8 1.8 - - + -
38A GLN 3.9 3.6 - - - +
39A THR* 3.4 25.1 + - - +
130A PHE* 3.6 3.4 - - - -
131A LYS* 2.8 39.5 + - + +
133A LYS* 3.1 33.0 + - - +
37B THR* 4.9 17.3 - - + +
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Residues in contact with MET 10 (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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9A GLU* 1.3 72.8 - - - +
11A GLU* 1.3 61.2 + - - +
12A SER 3.9 14.1 - - - +
13A ASN* 3.8 22.9 - - - +
36A LEU 4.8 5.6 - - - +
37A THR* 5.7 1.1 - - + -
38A GLN* 3.1 61.1 + - + +
128A GLN* 3.7 22.2 - - + +
129A VAL 3.5 6.5 - - - +
130A PHE* 3.3 28.9 - - + -
35B ARG* 3.9 10.2 - - - +
37B THR* 3.5 24.8 + - + +
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Residues in contact with GLU 11 (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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9A GLU* 4.0 9.4 - - + +
10A MET* 1.3 75.3 - - - +
12A SER* 1.3 60.2 + - - +
114A LYS* 3.0 31.8 + - - +
129A VAL* 2.6 20.1 + - + +
130A PHE 4.6 0.7 - - - -
131A LYS* 3.5 19.5 - - + +
32B ILE 4.6 2.9 - - - +
35B ARG* 3.4 21.3 + - - +
36B LEU* 3.4 25.5 - - + +
37B THR* 4.9 3.1 - - - +
56B THR* 2.9 41.5 + - + +
57B PHE* 4.3 7.6 - - - -
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Residues in contact with SER 12 (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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10A MET* 3.8 6.9 - - - +
11A GLU* 1.3 83.9 - - - +
13A ASN* 1.3 66.7 + - - +
14A GLU* 4.9 4.3 + - - +
127A ARG 4.5 2.0 + - - -
128A GLN* 3.4 5.1 - - - -
129A VAL* 3.2 46.4 + - - +
31B LYS 5.4 4.3 + - - -
35B ARG* 4.3 3.8 - - - -
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Residues in contact with ASN 13 (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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10A MET* 3.8 20.9 - - - +
12A SER* 1.3 76.0 + - - +
14A GLU* 1.3 60.8 + - - +
15A ASN 4.1 0.5 + - - -
16A PHE* 2.9 46.3 + - - +
38A GLN* 4.2 0.2 - - - +
126A CYS* 3.1 26.9 - - - -
127A ARG 3.9 1.6 - - - -
128A GLN* 3.2 18.8 - - - +
35B ARG* 3.0 50.5 + - + +
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Residues in contact with GLU 14 (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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12A SER* 4.2 4.4 + - - +
13A ASN* 1.3 70.5 - - - +
15A ASN* 1.3 73.9 + - + +
16A PHE 3.3 1.7 + - - -
126A CYS* 3.4 2.3 - - - -
127A ARG* 3.0 41.4 + - + +
31B LYS* 5.2 11.9 - - - +
35B ARG* 4.9 2.2 - - - +
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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