Contacts of the strand formed by residues 58 - 68 (chain S) 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 VAL 58 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34S GLU* 3.5 30.1 - - + +
35S PHE 3.7 6.5 - - - +
36S ALA* 3.7 22.2 - - + +
38S VAL* 4.3 0.8 - - - +
56S GLY 3.3 10.7 + - - +
57S GLY* 1.3 79.9 - - - +
59S ILE* 1.3 80.2 + - - +
60S LYS* 3.8 6.3 + - + +
100S GLY 4.0 0.3 - - - +
101S ILE* 5.8 0.2 - - - -
102S SER* 2.9 41.5 + - - +
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Residues in contact with ILE 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S ALA* 4.6 6.3 - - + -
5S PHE* 3.6 45.5 - - + -
14S VAL* 4.8 3.1 - - + -
33S VAL 4.0 0.3 - - - +
34S GLU* 3.4 4.9 - - - -
35S PHE* 2.9 44.0 + - + +
38S VAL* 4.5 18.8 - - + -
41S ILE* 6.4 0.4 - - + -
58S VAL* 1.3 79.3 - - - +
60S LYS* 1.3 62.8 + - - +
61S ALA* 4.9 1.3 - - + +
98S ILE* 3.7 31.6 - - + -
100S GLY 3.3 15.9 - - - +
101S ILE* 3.8 19.7 - - + -
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Residues in contact with LYS 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S THR* 3.3 29.4 + - + +
33S VAL 3.8 2.0 - - - -
34S GLU* 3.2 35.1 + - + +
58S VAL* 3.8 6.6 + - + +
59S ILE* 1.3 74.2 - - - +
61S ALA* 1.3 56.0 + - - +
98S ILE* 4.1 1.4 - - - +
99S THR* 2.6 27.7 + - - +
100S GLY* 2.9 29.6 + - - +
102S SER* 5.8 4.3 - - - +
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Residues in contact with ALA 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S THR* 3.3 9.7 - - - +
33S VAL* 2.9 47.3 + - + +
35S PHE* 4.0 11.7 - - + -
59S ILE* 5.0 0.7 - - + -
60S LYS* 1.3 75.0 - - - +
62S GLU* 1.3 60.9 + - - +
96S VAL* 4.4 5.6 - - + -
97S LYS 3.7 5.2 - - - +
98S ILE* 3.6 29.4 - - + -
99S THR* 3.7 5.8 - - - +
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Residues in contact with GLU 62 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30S GLY* 3.6 29.0 - - - +
31S GLU 3.6 4.9 - - - +
32S THR* 5.2 3.6 - - - +
61S ALA* 1.3 75.1 - - - +
63S VAL* 1.3 65.3 + - - +
64S VAL* 3.4 8.9 + - + +
96S VAL* 3.2 8.9 - - - -
97S LYS* 3.0 39.0 + - + +
99S THR* 3.6 24.5 - - + +
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Residues in contact with VAL 63 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25S LEU* 4.8 1.8 - - + -
27S ILE* 3.8 14.8 - - + +
28S ALA 3.9 7.6 - - - +
29S THR* 3.4 17.6 - - + +
30S GLY* 2.5 32.1 + - - -
31S GLU 3.0 14.0 + - - +
33S VAL* 3.6 29.8 - - + -
62S GLU* 1.3 71.3 - - - +
64S VAL* 1.3 61.3 + - - +
65S ALA 4.3 5.6 - - - +
66S HIS* 3.8 20.0 - - - +
94S THR* 4.1 17.0 - - + -
96S VAL* 3.8 15.5 - - + -
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Residues in contact with VAL 64 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S THR* 4.3 7.4 - - + +
29S THR* 3.1 15.7 - - - +
62S GLU* 3.9 11.7 - - + +
63S VAL* 1.3 75.0 - - - +
65S ALA* 1.3 67.4 + - + +
95S ASP* 3.1 38.2 + - + +
96S VAL* 3.9 3.6 - - - +
97S LYS* 3.7 31.4 - - + +
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Residues in contact with ALA 65 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S THR* 4.1 6.2 - - - +
63S VAL* 3.7 1.4 - - - -
64S VAL* 1.3 90.2 - - + +
66S HIS* 1.3 71.3 + - - +
93S PHE* 5.0 4.5 - - + -
94S THR* 3.5 6.1 - - - +
95S ASP* 2.9 32.6 + - + +
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Residues in contact with HIS 66 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24S LYS* 5.0 5.0 - - + +
25S LEU 3.2 26.7 + - - -
26S ASP* 5.2 0.2 - - - -
27S ILE* 3.1 23.6 + - + -
29S THR* 3.0 26.7 + - - -
63S VAL* 3.8 6.4 - - + +
65S ALA* 1.3 81.9 - - - +
67S GLY* 1.3 60.6 + - - +
92S TRP* 5.2 6.8 - - + -
93S PHE* 3.6 16.5 + - - -
94S THR* 3.0 28.3 + - + -
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Residues in contact with GLY 67 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66S HIS* 1.3 78.7 - - - +
68S ARG* 1.3 60.2 + - - -
92S TRP* 3.0 28.6 - - - -
93S PHE* 2.9 41.0 + - - -
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Residues in contact with ARG 68 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1223A G 2.9 39.4 + - - -
1224A U 2.3 34.9 + - - -
67S GLY* 1.3 79.2 - - - +
69S GLY* 1.3 65.5 + - - +
90S ARG* 2.9 85.1 + - + +
91S GLN 3.7 3.1 - - - -
92S TRP* 3.5 44.7 - - + +
93S PHE* 3.3 6.5 - - - -
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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