Contacts of the strand formed by residues 13 - 20 (chain D) in PDB entry 2G94
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 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ARG 4.0 0.2 - - - +
8D GLY* 3.3 8.5 - - - -
9D LYS 2.8 33.6 + - - -
11D GLY 3.7 1.2 - - - -
12D GLN* 1.3 77.5 - - - +
14D TYR* 1.3 60.5 + - - -
15D TYR* 4.0 7.3 - - - -
30D LEU* 3.5 8.1 - - - -
113D SER 5.1 0.7 - - - +
115D TRP* 4.7 1.1 - - - -
4001D ZPQ 3.4 25.6 - - - -
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Residues in contact with TYR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 4.6 7.6 - - + -
7D ARG 3.3 8.1 - - - +
8D GLY 3.8 12.3 - - - -
9D LYS* 3.5 27.5 - - - -
10D SER* 3.7 8.1 + - - -
13D GLY* 1.3 74.5 - - - -
15D TYR* 1.3 61.4 + - - +
30D LEU* 3.5 6.5 - - - +
31D VAL* 2.9 31.1 + - + +
154D LEU* 3.7 46.4 - - + -
155D CYS 3.2 20.4 + - - -
156D GLY* 3.8 1.0 - - - -
171D GLY 3.1 29.8 - - - -
229D SER* 5.0 2.4 + - - +
335D ALA* 4.7 1.6 - - + -
339D GLU* 2.5 29.4 + - - +
4001D ZPQ 4.4 13.3 - - + +
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Residues in contact with TYR 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN 4.0 0.2 - - - +
6D LEU* 3.4 10.4 - - - -
7D ARG* 2.9 78.9 + - + +
8D GLY* 4.0 7.3 + - - -
13D GLY 4.0 8.5 - - - -
14D TYR* 1.3 75.0 - - - +
16D VAL* 1.3 60.8 - - - +
28D ASN* 3.5 36.8 - - + -
29D ILE 3.1 21.5 - - - +
30D LEU* 3.8 4.0 - - - +
31D VAL* 4.3 0.9 - - - +
113D SER 3.3 24.9 - - - -
114D ASN* 2.8 27.0 + - + +
115D TRP* 3.9 14.1 - + + -
166D VAL* 5.0 5.1 + - + +
167D LEU* 4.1 5.5 - - - +
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN* 3.9 25.8 - - + +
6D LEU* 3.7 13.9 - - + -
15D TYR* 1.3 75.4 - - - +
17D GLU* 1.3 71.0 + - - +
18D MET* 3.7 18.3 + - + -
28D ASN* 4.6 3.4 - - - -
29D ILE* 2.8 41.6 + - + +
31D VAL* 4.2 5.2 - - + -
87D ILE* 4.1 13.7 - - + -
89D HIS* 5.8 2.0 - - + -
119D LEU* 4.9 3.8 - - + -
174D MET* 3.9 27.1 - - + -
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Residues in contact with GLU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ASN 4.6 3.4 + - - +
7D ARG* 5.6 3.3 + - - -
15D TYR* 5.2 0.4 - - - -
16D VAL* 1.3 76.8 - - + +
18D MET* 1.3 70.5 + - - +
26D THR* 3.6 30.0 + - + +
27D LEU 3.7 3.6 - - - -
28D ASN* 3.9 16.0 + - - +
50D ARG* 5.1 1.0 + - - -
87D ILE* 3.7 10.9 - - - +
88D PRO* 3.3 38.7 - - + +
89D HIS* 4.6 19.1 + - + -
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Residues in contact with MET 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D VAL* 4.1 14.4 - - + -
17D GLU* 1.3 80.3 - - - +
19D THR* 1.3 69.2 + - - +
20D VAL* 5.3 3.8 - - + -
26D THR* 3.4 6.1 - - - +
27D LEU* 2.8 31.3 + - - -
29D ILE* 3.6 41.3 - - + -
38D PHE* 4.0 12.1 - - + -
85D VAL* 3.4 31.2 - - + -
86D SER 3.4 7.9 - - - +
87D ILE* 3.8 16.2 - - + -
88D PRO* 3.9 2.2 - - - -
119D LEU* 4.5 8.5 - - + -
136D PHE* 3.6 28.7 - - + -
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Residues in contact with THR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET* 1.3 79.5 - - - +
20D VAL* 1.3 66.2 + - - +
21D GLY 5.5 0.7 + - - -
24D PRO* 3.9 26.2 - - + +
25D GLN 3.1 7.9 - - - -
26D THR* 4.0 17.3 - - - +
85D VAL* 3.3 6.2 - - - +
86D SER* 2.9 46.1 + - - +
88D PRO* 3.8 22.9 - - + -
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Residues in contact with VAL 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET* 5.3 3.4 - - + -
19D THR* 1.3 81.3 - - - +
21D GLY* 1.3 62.9 + - - +
25D GLN* 2.9 37.4 + - + +
27D LEU* 3.6 27.4 - - + -
29D ILE* 6.1 0.4 - - + -
38D PHE* 4.2 18.4 - - + -
40D VAL* 5.1 2.7 - - + -
52D TYR* 3.5 31.4 - - + -
84D LEU 3.3 6.1 - - - +
85D VAL* 4.1 16.4 - - + -
99D ILE* 4.3 14.1 - - + -
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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