Contacts of the strand formed by residues 21 - 28 (chain D) in PDB entry 5GAG
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 SER 21 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2729A G 4.2 5.2 + - - -
13D ARG* 3.1 39.1 + - - +
14D ILE 3.5 4.7 + - - -
15D PHE* 3.8 19.5 - - - -
20D VAL* 1.3 75.9 - - - +
22D ILE* 1.3 60.5 + - - +
23D PRO* 3.2 12.3 - - - +
72L PRO 3.2 15.0 + - - +
73L ASP* 3.8 18.7 - - - +
74L GLY* 5.5 0.2 - - - -
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Residues in contact with ILE 22 (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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2729A G 5.1 0.7 - - - +
14D ILE* 2.7 45.6 + - + +
16D THR* 3.9 23.3 - - + -
20D VAL* 4.6 7.0 - - + +
21D SER* 1.3 75.8 - - - +
23D PRO* 1.3 63.7 - - + +
24D VAL* 3.4 8.2 - - + +
178D VAL* 4.3 24.5 - - + -
190D LYS* 3.6 48.0 - - + +
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Residues in contact with PRO 23 (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 3.5 45.1 - - + +
2728A U 4.1 5.2 - - - +
2729A G 3.4 28.5 - - - +
11D MET* 4.5 5.8 - - + -
12D THR 3.6 9.2 - - - +
13D ARG* 4.3 3.8 - - + -
21D SER* 3.2 13.0 - - - +
22D ILE* 1.3 85.7 - - + +
24D VAL* 1.3 58.7 + - - +
190D LYS* 3.4 6.8 - - + +
191D GLY* 3.1 26.9 + - - +
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Residues in contact with VAL 24 (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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11D MET* 3.5 11.3 - - - +
12D THR* 3.1 32.1 + - + +
14D ILE* 3.6 26.9 - - + +
22D ILE 3.4 18.4 - - - +
23D PRO* 1.3 74.4 - - - +
25D THR* 1.3 76.5 + - - +
26D VAL* 4.2 11.4 - - + -
178D VAL* 4.6 16.4 - - + -
188D LEU* 4.0 15.5 - - + -
189D VAL 3.2 17.7 - - - +
191D GLY 4.2 0.7 - - - -
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Residues in contact with THR 25 (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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8D LYS* 3.6 25.8 - - + -
10D GLY 3.6 10.3 - - - +
11D MET* 3.8 10.3 - - + +
24D VAL* 1.3 76.9 + - - +
26D VAL* 1.3 68.5 + - - +
27D ILE* 3.9 2.9 - - + -
187D LEU 3.5 0.5 - - - +
188D LEU* 3.4 4.7 - - - -
189D VAL* 2.9 37.3 + - - +
191D GLY 3.2 17.5 + - - -
193D VAL* 3.5 42.8 + - + +
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Residues in contact with VAL 26 (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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8D LYS* 3.9 2.4 - - - -
9D VAL* 2.9 41.7 + - + +
10D GLY 2.9 20.0 + - - +
12D THR* 3.6 25.6 - - + -
24D VAL* 4.2 1.8 - - + -
25D THR* 1.3 74.1 - - - +
27D ILE* 1.3 59.2 + - - +
186D LEU* 3.6 24.9 - - + -
188D LEU* 3.5 30.1 - - + -
4Q ILE* 4.4 4.7 - - + -
5Q ILE* 4.2 7.2 - - + -
8Q LEU* 4.3 10.5 - - + -
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Residues in contact with ILE 27 (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* 4.1 11.7 - - - -
7D LYS 3.8 22.0 - - - +
8D LYS* 5.2 0.4 - - - -
25D THR* 4.6 5.4 - - + +
26D VAL* 1.3 74.5 - - - +
28D GLU* 1.3 64.8 + - - +
29D VAL* 3.6 8.9 + - + -
109D VAL* 4.3 11.7 - - + -
186D LEU* 3.7 4.4 - - - -
187D LEU* 2.9 46.1 + - + +
189D VAL* 4.1 25.8 - - + -
193D VAL* 4.8 1.1 - - + -
201D LEU* 3.6 30.5 - - + -
203D VAL* 4.1 26.0 - - + -
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Residues in contact with GLU 28 (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* 3.1 4.5 - - - -
7D LYS* 2.9 73.4 + - - +
9D VAL* 3.7 11.3 - - + +
26D VAL 3.9 1.4 + - - -
27D ILE* 1.3 72.0 - - - +
29D VAL* 1.3 64.8 + - - +
30D GLU* 4.0 19.2 + - + +
184D ARG 5.3 1.7 - - - +
185D ASN* 3.6 15.5 - - + +
186D LEU* 4.4 5.4 - - + -
4Q ILE* 3.1 30.4 - - + +
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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