Contacts of the strand formed by residues 100 - 108 (chain T) 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 THR 100 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9T HIS* 3.9 22.4 - - + +
10T ALA 3.2 12.1 - - - +
11T ARG* 4.6 20.4 - - + +
12T SER 3.1 10.3 - - - +
14T ALA 4.3 3.8 + - - -
78T GLU* 4.5 3.5 - - - +
79T GLY* 3.1 27.0 + - - +
80T PRO* 2.8 34.4 + - + +
81T SER* 4.1 2.2 + - - -
82T MET* 4.8 9.0 - - + -
98T LYS 4.6 3.8 - - - +
99T ARG* 1.3 81.3 - - - +
101T SER* 1.3 63.4 + - - +
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Residues in contact with SER 101 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7T HIS 4.0 0.9 - - - +
9T HIS 3.5 1.4 + - - -
10T ALA* 3.0 33.7 + - - +
12T SER* 3.6 13.6 + - - -
13T SER 4.0 3.2 + - - -
14T ALA* 3.9 17.0 - - - -
17T VAL* 4.1 12.6 - - - +
76T VAL* 4.0 5.4 - - - -
77T ASP 3.4 13.7 - - - -
79T GLY 3.9 3.1 - - - +
100T THR* 1.3 79.9 + - - +
102T HIS* 1.3 68.2 + - - +
103T ILE* 3.8 6.9 + - - +
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Residues in contact with HIS 102 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A G 3.5 29.8 + - - -
25A U 3.3 10.5 + - - -
7T HIS 3.6 4.0 - - - +
8T ARG* 3.3 39.6 + - + -
9T HIS* 3.5 24.7 + + - -
75T PHE 3.5 1.9 - - - +
76T VAL* 3.2 6.3 - - - -
77T ASP* 2.9 44.3 + - + +
79T GLY* 3.8 19.8 - - - -
80T PRO* 3.9 9.6 - - + -
101T SER* 1.3 78.6 + - - +
103T ILE* 1.3 63.5 + - - +
104T THR* 3.6 7.9 + - - +
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Residues in contact with ILE 103 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5T ALA 3.8 1.0 - - - +
6T LYS* 3.4 2.9 - - - -
7T HIS* 2.9 56.2 + - + +
10T ALA* 4.0 12.1 - - + -
17T VAL* 4.3 14.6 - - + -
21T ALA* 5.8 0.2 - - + -
46T LEU* 3.9 32.1 - - + -
47T VAL* 4.4 18.8 - - + +
50T VAL* 4.2 10.0 - - + +
74T ILE* 5.4 3.1 - - + -
75T PHE 3.9 2.5 - - - +
76T VAL* 4.2 13.7 - - + -
101T SER* 4.2 12.6 - - - +
102T HIS* 1.3 73.4 - - - +
104T THR* 1.3 63.7 + - - +
105T VAL* 4.1 17.0 + - + -
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Residues in contact with THR 104 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T ILE* 3.9 15.0 - - + -
5T ALA 3.6 2.7 - - - +
6T LYS* 3.8 31.1 - - + +
73T LYS 4.1 0.3 - - - +
74T ILE* 3.4 4.4 - - - +
75T PHE* 2.9 74.0 + - + +
77T ASP* 5.1 1.4 + - - -
102T HIS* 4.0 10.6 + - - +
103T ILE* 1.3 75.1 - - - +
105T VAL* 1.3 65.6 + - - +
106T VAL* 4.5 2.7 - - + -
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Residues in contact with VAL 105 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3T THR 4.1 0.2 - - - +
4T ILE* 3.4 0.7 - - - +
5T ALA 2.9 33.7 + - - +
47T VAL* 5.0 3.6 - - + +
50T VAL* 3.5 30.3 - - + -
51T LEU* 3.6 32.1 - - + +
54T ALA* 4.7 6.6 - - + +
71T VAL* 4.3 11.0 - - + -
73T LYS 3.7 5.8 - - - +
74T ILE* 4.0 19.3 - - + +
103T ILE* 4.4 7.0 - - + -
104T THR* 1.3 79.6 - - - +
106T VAL* 1.3 67.5 + - - +
107T VAL* 4.2 11.7 - - + -
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Residues in contact with VAL 106 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T GLU* 3.5 42.0 - - + +
3T THR 3.5 8.1 - - - +
4T ILE* 3.6 26.9 - - + -
71T VAL* 4.1 0.5 - - - -
72T THR* 2.9 22.9 + - - +
73T LYS* 2.8 46.2 + - + +
75T PHE* 4.8 4.7 - - + -
104T THR* 4.5 8.5 - - + -
105T VAL* 1.3 79.7 - - - +
107T VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 107 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T MET 3.8 0.2 - - - +
2T GLU* 3.6 1.0 - - - -
3T THR* 2.9 52.2 + - - +
29T VAL* 4.5 7.0 - - + -
51T LEU* 4.5 4.9 - - + -
54T ALA* 4.3 26.0 - - + +
55T ILE* 5.0 3.1 - - + +
58T ALA* 4.6 2.5 - - + -
69T LEU* 4.1 20.9 - - + -
70T LYS 3.5 15.0 - - - +
71T VAL* 4.3 16.8 - - + -
72T THR* 3.7 0.7 - - - -
105T VAL* 4.3 11.9 - - + -
106T VAL* 1.3 79.1 - - - +
108T SER* 1.3 63.6 + - - +
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Residues in contact with SER 108 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1T MET 3.2 26.2 - - - -
2T GLU* 4.1 11.1 + - - +
69T LEU* 3.4 8.3 - - - -
70T LYS* 3.0 29.4 + - - +
72T THR* 3.2 22.3 + - - +
107T VAL* 1.3 76.3 - - - +
109T ASP* 1.3 63.6 + - - +
110T ARG* 2.9 23.9 + - - -
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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