Contacts of the strand formed by residues 4 - 15 (chain D) in PDB entry 5GAH
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 LEU 4 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D ILE* 5.2 0.2 - - + -
3D GLY* 1.3 84.5 - - - +
5D VAL* 1.3 65.9 + - - +
6D GLY 4.0 0.5 + - - -
29D VAL* 3.8 20.6 - - + -
32D ASN* 3.5 19.5 - - + +
50D VAL* 6.4 0.2 - - + -
82D PHE* 4.4 1.3 - - - -
96D ILE* 3.5 29.6 - - + -
97D SER 3.6 21.3 - - - +
98D VAL* 3.6 14.1 - - + -
100D LEU* 4.2 9.6 - - + -
101D PHE* 3.5 30.1 - - + -
201D LEU 3.7 0.7 - - - +
202D ILE* 3.5 2.8 - - - +
203D VAL* 2.8 35.3 + - + +
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Residues in contact with VAL 5 (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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4D LEU* 1.3 77.2 - - - +
6D GLY* 1.3 66.1 + - - +
29D VAL* 3.2 15.6 - - - +
30D GLU 4.3 0.2 - - - +
32D ASN* 2.7 22.4 + - - +
50D VAL* 5.0 1.6 - - + -
51D THR 6.2 0.2 - - - -
52D THR* 3.7 30.8 + - + +
80D TRP* 3.7 50.7 - - + +
82D PHE* 3.8 17.3 - - + -
200D ASP* 4.7 6.7 - - + +
201D LEU 3.3 7.9 - - - +
202D ILE* 3.9 12.3 - - + -
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Residues in contact with GLY 6 (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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4D LEU 4.0 0.8 + - - -
5D VAL* 1.3 74.5 - - - +
7D LYS* 1.3 60.5 + - - +
27D ILE* 4.0 13.6 - - - +
28D GLU 3.2 14.8 - - - -
29D VAL* 4.1 5.6 - - - -
30D GLU 5.4 0.2 - - - -
77D ARG* 4.5 6.5 - - - -
200D ASP* 3.6 6.8 - - - +
201D LEU* 2.8 30.5 + - - -
203D VAL* 5.8 0.8 - - - +
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Residues in contact with LYS 7 (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 GLY* 1.3 75.2 - - - +
8D LYS* 1.3 68.4 + - - +
9D VAL* 3.3 3.9 + - + +
27D ILE* 3.3 3.9 - - - +
28D GLU* 2.9 54.7 + - - +
77D ARG* 3.2 36.8 - - - +
198D GLY* 3.6 28.9 - - - +
199D SER 3.3 15.5 - - - +
200D ASP* 4.5 2.5 - - - +
201D LEU* 3.9 4.5 - - - -
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2680A U 3.4 21.0 + - - -
2681A C 3.9 11.2 - - - -
7D LYS* 1.3 71.2 - - - +
9D VAL* 1.3 63.2 + - - +
10D GLY* 3.9 9.6 - - - +
11D MET* 4.6 15.6 - - - +
25D THR* 4.1 12.3 - - + +
26D VAL 3.9 3.4 - - - -
27D ILE* 5.1 0.2 - - - -
193D VAL* 3.0 41.5 + - + +
194D PRO 4.3 0.9 - - - +
195D GLY 3.1 26.1 + - - +
196D ALA 4.1 9.4 - - - +
197D THR* 3.5 13.2 - - - +
198D GLY 3.0 23.9 + - - -
199D SER* 3.0 13.3 + - - +
201D LEU* 3.5 19.2 - - + +
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Residues in contact with VAL 9 (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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7D LYS* 3.8 3.6 - - + +
8D LYS* 1.3 73.9 - - - +
10D GLY* 1.3 58.6 + - - +
26D VAL* 2.9 31.3 + - + +
28D GLU* 3.6 35.9 - - + +
197D THR* 3.3 18.5 - - - +
2Q SER 4.2 12.6 + - - +
4Q ILE* 4.3 21.1 - - + -
5Q ILE* 3.4 28.2 - - + +
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Residues in contact with GLY 10 (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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2682A A 6.0 0.4 - - - -
8D LYS* 3.4 8.9 - - - +
9D VAL* 1.3 81.8 - - - +
11D MET* 1.3 65.6 + - - -
25D THR* 3.7 6.3 - - - +
26D VAL* 3.0 25.3 + - - +
197D THR* 3.9 13.0 - - - -
5Q ILE* 3.7 10.5 - - - -
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Residues in contact with MET 11 (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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2680A U 3.4 25.4 - - - +
2681A C 3.8 16.6 - - - +
2682A A 3.4 61.0 + - + +
8D LYS* 4.6 11.2 - - - +
10D GLY* 1.3 78.4 - - - +
12D THR* 1.3 68.7 + - - +
23D PRO* 4.5 9.9 - - + -
24D VAL 3.2 17.9 - - - +
25D THR* 3.8 17.5 - - - +
191D GLY 4.0 15.3 - - - +
192D ALA* 4.5 4.0 - - + -
5Q ILE* 4.4 9.5 - - - +
9Q GLU* 4.6 1.9 - - - +
56Q HIS* 5.1 0.2 + - - -
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Residues in contact with THR 12 (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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2682A A 3.7 17.9 - - - -
11D MET* 1.3 78.6 - - - +
13D ARG* 1.3 86.7 + - - +
14D ILE* 4.7 4.1 - - + +
23D PRO* 3.7 4.3 - - - +
24D VAL* 2.9 41.7 + - + +
26D VAL* 3.7 16.4 - - + -
5Q ILE* 4.2 11.4 - - + -
8Q LEU* 5.4 7.4 - - + -
9Q GLU* 3.8 19.9 - - + +
12Q GLN* 4.9 0.3 + - - -
55Q LEU* 3.8 12.6 - - - +
56Q HIS* 4.1 3.3 - - - -
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Residues in contact with ARG 13 (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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2682A A 4.1 8.8 + - - +
2683A C 3.2 43.9 + - - -
12D THR* 1.3 95.4 + - - +
14D ILE* 1.3 71.7 + - - +
15D PHE* 3.2 35.2 - - + -
21D SER* 3.3 28.8 + - - +
22D ILE 3.5 9.0 - - - +
23D PRO* 4.8 1.8 - - + -
73L ASP 4.0 4.2 + - - -
74L GLY* 5.3 0.2 - - - -
12Q GLN* 3.2 9.9 + - - -
55Q LEU* 3.8 11.3 + - + +
56Q HIS* 3.6 38.0 + - + +
75Q GLN* 3.0 34.9 + - - +
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Residues in contact with ILE 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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12D THR* 4.7 6.3 - - + +
13D ARG* 1.3 84.6 - - - +
15D PHE* 1.3 74.7 + - - +
16D THR* 5.8 0.2 - - + -
20D VAL 3.5 1.7 - - - +
21D SER* 4.7 0.4 - - - -
22D ILE* 3.1 40.0 + - + +
24D VAL* 3.6 27.1 - - + -
178D VAL* 4.7 11.0 - - + -
179D ARG* 3.9 24.2 - - - +
188D LEU* 4.1 22.0 - - + -
8Q LEU* 5.4 8.5 - - + +
12Q GLN* 3.3 21.5 - - - +
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Residues in contact with PHE 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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13D ARG* 3.2 39.3 - - + -
14D ILE* 1.3 87.7 - - - +
16D THR* 1.3 63.6 + - - +
20D VAL 3.3 8.1 - - - -
21D SER* 3.9 19.7 - - - -
73L ASP* 4.5 7.0 - - + -
12Q GLN* 3.0 23.4 + - + +
55Q LEU* 3.7 28.5 - - + -
75Q GLN* 4.6 4.9 - - + -
77Q HIS* 4.0 15.9 - - + -
78Q SER* 3.7 27.4 - - - -
79Q PRO* 3.8 24.9 - - + -
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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