Contacts of the strand formed by residues 109 - 115 (chain O) 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 PRO 109 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1650A A 3.8 11.4 - - - +
37O THR* 3.5 8.7 - - - -
38O LEU* 3.0 39.6 + - + -
39O PRO* 4.8 3.7 - - + +
100O CYS 5.6 0.4 - - - +
102O PHE* 3.7 28.0 - - + -
107O ASN 3.8 7.0 - - - +
108O ALA* 1.3 86.8 - - + +
110O MET* 1.3 60.0 + - - +
42b HIS* 6.6 0.7 - - + -
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Residues in contact with MET 110 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O LYS* 3.7 33.7 - - + +
36O THR* 3.6 25.6 - - - +
37O THR* 3.9 10.8 - - - -
38O LEU* 4.3 5.7 - - - +
99O LYS* 3.7 4.3 - - - +
100O CYS* 3.1 35.3 + - - +
101O GLY 3.1 16.5 + - - +
102O PHE 4.2 0.7 - - - -
103O ARG* 3.6 53.6 - - + +
108O ALA* 3.4 13.7 - - - +
109O PRO* 1.3 80.1 - - - +
111O ALA* 1.3 62.7 + - - +
42b HIS* 5.7 0.2 - - - -
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Residues in contact with ALA 111 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35O LYS* 3.4 1.4 - - - -
36O THR* 2.9 37.3 + - - +
38O LEU* 3.6 22.4 - - + +
41O ALA* 4.5 4.9 - - + -
97O ILE* 3.5 28.0 - - + -
98O LEU 3.4 8.3 - - - +
99O LYS* 4.3 2.0 - - - -
100O CYS* 3.6 5.6 - - - -
110O MET* 1.3 77.5 - - - +
112O TYR* 1.3 61.4 + - - +
113O ILE 3.7 1.0 + - - -
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Residues in contact with TYR 112 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33O ILE* 3.9 24.5 - - + -
34O ILE 3.2 11.2 - - - +
35O LYS* 3.6 39.3 + - + +
96O ARG 3.6 1.6 - - - +
97O ILE* 3.3 4.2 - - - -
98O LEU* 2.9 38.7 + - + +
100O CYS* 3.8 17.7 - - + -
111O ALA* 1.3 71.5 - - - +
113O ILE* 1.3 61.1 + - - +
114O GLU* 5.3 0.2 - - - -
43b ILE* 3.5 31.0 - - + -
55b ILE* 4.2 20.9 - - + +
57b LYS* 4.2 28.3 + - + +
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Residues in contact with ILE 113 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28O LEU* 3.8 17.2 - - + +
33O ILE* 3.4 0.9 - - - +
34O ILE* 2.9 61.9 + - + +
36O THR* 4.4 8.1 - - + -
41O ALA* 3.7 27.6 - - + +
44O LEU* 4.6 11.0 - - + -
45O ARG* 4.0 15.9 - - + +
95O THR* 4.2 12.6 - - + -
96O ARG 3.5 3.4 - - - +
97O ILE* 3.6 29.2 - - + -
111O ALA 3.7 2.0 + - - -
112O TYR* 1.3 73.7 - - - +
114O GLU* 1.3 67.2 + - - +
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Residues in contact with GLU 114 (chain O).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28O LEU* 3.9 4.0 - - - -
32O GLU 3.5 13.5 - - - +
33O ILE* 3.7 16.8 - - + +
95O THR* 3.2 6.8 - - - -
96O ARG* 2.9 55.7 + - + +
98O LEU* 3.3 25.5 - - + +
112O TYR 5.1 0.2 - - - +
113O ILE* 1.3 79.9 - - - +
115O LEU* 1.3 73.6 + - - +
118O ARG* 2.6 38.3 + - - +
119O SER* 5.1 0.9 + - - -
54b VAL* 4.2 6.5 - - - +
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Residues in contact with LEU 115 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28O LEU* 3.8 29.6 - - + +
29O VAL* 4.9 0.4 - - - +
32O GLU* 3.2 33.1 + - + +
48O VAL* 4.9 2.7 - - + -
52O ILE* 4.3 18.8 - - + -
83O LEU* 4.3 26.7 - - + -
86O ARG* 5.1 1.6 - - - +
87O PHE* 4.0 11.7 - - + -
94O TYR 3.3 12.3 - - - +
95O THR* 4.0 15.9 - - + -
96O ARG* 4.3 0.4 - - - -
114O GLU* 1.3 93.6 - - - +
116O VAL* 1.3 64.7 + - - +
117O ASP 3.4 2.6 + - - +
118O ARG* 3.7 14.8 - - + +
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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