Contacts of the strand formed by residues 71 - 79 (chain T) in PDB entry 2A2Q
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 TYR 71 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14T TRP* 4.5 7.6 - - + -
38T ILE* 3.9 27.8 - - + -
39T SER* 3.2 10.8 - - - +
40T THR* 3.6 23.8 - - + -
62T GLU* 3.6 16.0 + - + -
63T ILE* 3.1 22.5 + - + -
65T LYS* 4.8 1.2 - - - +
66T ASP* 2.6 39.2 + - - +
69T GLN* 3.6 21.1 - - + +
70T THR* 1.3 75.7 - - - +
72T LEU* 1.3 61.1 + - - +
98T PRO 4.2 0.3 - - - +
99T GLU* 3.3 5.6 - - - +
100T PHE* 2.8 43.9 + - + +
102T PRO* 3.7 18.8 - - + -
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Residues in contact with LEU 72 (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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14T TRP* 4.7 1.1 - - - -
38T ILE* 3.5 3.1 - - - +
39T SER* 2.9 31.8 + - - +
40T THR 6.2 1.6 - - - -
45T TRP* 3.7 23.8 - - + -
71T TYR* 1.3 74.1 - - - +
73T ALA* 1.3 86.9 + - - +
96T ASN* 3.9 22.2 - - + +
97T SER* 2.9 27.6 - - - +
98T PRO 3.7 3.8 - - - +
99T GLU* 3.7 31.6 - - + +
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Residues in contact with ALA 73 (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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14T TRP* 4.0 15.0 - - + -
23T LEU* 4.0 21.1 - - + -
36T VAL* 4.5 0.9 - - + -
37T GLN 3.0 15.3 - - - +
38T ILE* 4.4 1.8 - - - -
45T TRP* 4.4 0.9 - - - -
59T LEU* 4.3 8.3 - - + -
72T LEU* 1.3 84.0 - - - +
74T ARG* 1.3 59.5 + - - +
97T SER* 2.7 44.0 + - - +
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Residues in contact with ARG 74 (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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129H PHE* 3.4 23.0 + - - -
164H MET* 3.5 29.2 - - - +
167H ASP* 3.9 14.1 + - - -
12T LEU* 4.6 0.4 - - - -
35T THR 4.0 0.5 - - - +
36T VAL* 3.4 3.8 - - - +
37T GLN* 2.9 58.1 + - + +
45T TRP* 3.4 51.4 - - + +
73T ALA* 1.3 76.6 - - - +
75T VAL* 1.3 65.0 + - - +
76T PHE* 3.6 17.7 + - + -
94T TYR* 4.2 8.7 - - + -
95T GLU 3.1 15.0 - - - +
96T ASN* 3.5 17.9 - - - +
97T SER 4.5 0.4 - - - +
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Residues in contact with VAL 75 (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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9T ALA* 3.7 22.1 + - + +
12T LEU* 3.6 23.1 - - + -
23T LEU* 3.7 19.1 - - + -
25T TRP* 3.8 28.3 - - + -
34T TYR* 3.6 34.5 - - + -
35T THR 3.6 4.3 - - - +
36T VAL* 4.3 2.7 - - + -
74T ARG* 1.3 76.1 - - - +
76T PHE* 1.3 63.4 + - - +
77T SER* 4.0 0.9 + - - -
94T TYR* 3.2 20.6 - - - -
95T GLU 2.9 10.4 + - - +
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Residues in contact with PHE 76 (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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129H PHE* 4.0 11.9 - - + -
164H MET* 3.6 25.8 - - + -
34T TYR* 3.1 29.6 - - - -
35T THR* 2.7 22.4 + - + +
37T GLN* 3.3 43.3 - - + -
74T ARG* 3.6 26.5 - - + -
75T VAL* 1.3 73.8 - - - +
77T SER* 1.3 60.9 + - - +
78T TYR* 3.2 38.0 - + + -
92T PRO* 3.8 16.4 - - + -
93T LEU 3.6 2.9 - - - -
94T TYR* 3.4 21.5 - + + -
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Residues in contact with SER 77 (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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6T THR* 3.8 21.7 - - - +
7T VAL 2.7 29.1 + - - -
8T ALA* 3.8 7.3 - - - -
9T ALA 3.9 2.4 + - - -
32T GLN* 4.1 7.0 - - - -
33T VAL 3.6 4.0 - - - -
34T TYR* 3.7 15.1 - - - -
75T VAL 4.8 0.9 + - - -
76T PHE* 1.3 72.5 - - - +
78T TYR* 1.3 61.0 + - - +
79T PRO* 4.6 0.7 - - - +
92T PRO* 3.6 19.4 - - - +
93T LEU* 2.9 17.8 + - - +
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Residues in contact with TYR 78 (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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129H PHE* 6.0 0.2 + - - -
6T THR* 3.5 4.9 - - - -
32T GLN* 3.0 5.0 - - - -
33T VAL* 2.8 49.6 + - + +
34T TYR 4.7 0.2 - - - -
35T THR* 3.7 32.2 - - + +
51T TYR* 4.1 25.3 + + - -
76T PHE* 3.2 34.0 - + + -
77T SER* 1.3 80.0 - - - +
79T PRO* 1.3 74.5 - - + +
82T ASN 4.5 9.2 - - - +
90T GLY 5.8 1.6 - - - -
92T PRO* 3.7 22.3 - - + +
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Residues in contact with PRO 79 (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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6T THR* 3.6 21.1 - - + +
31T ASN 3.8 7.0 - - - +
33T VAL* 4.9 0.4 - - - +
77T SER 4.6 1.1 - - - +
78T TYR* 1.3 93.3 - - + +
80T ALA* 1.3 68.7 + - - +
81T GLY 3.4 2.4 + - - -
82T ASN* 3.5 23.0 + - + +
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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