Contacts of the strand formed by residues 32 - 40 (chain T) in PDB entry 4IBL
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 GLN 32 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6T THR* 3.2 11.9 - - + -
7T VAL* 2.8 57.8 + - - +
27T PRO* 4.7 1.4 - - - +
29T PRO* 3.1 32.7 - - + +
30T VAL 3.8 12.9 - - - +
31T ASN* 1.3 80.3 + - - +
33T VAL* 1.3 69.4 + - - +
34T TYR* 3.0 31.6 + - + -
53T THR* 4.5 2.1 - - - +
77T SER* 3.8 4.2 + - - -
78T TYR 3.1 19.5 - - - +
79T PRO* 4.5 1.6 - - + -
80T ALA 4.1 2.2 - - - +
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Residues in contact with VAL 33 (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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29T PRO* 5.0 0.2 - - - -
32T GLN* 1.3 79.9 - - - +
34T TYR* 1.3 66.1 - - - +
51T TYR* 3.9 33.2 - - + +
52T THR 3.5 9.6 - - - +
53T THR* 3.8 20.4 - - + -
77T SER* 3.6 3.8 - - - -
78T TYR* 2.9 47.0 + - + +
79T PRO 5.1 2.0 - - - +
80T ALA* 5.6 6.7 - - + -
82T ASN 4.4 8.7 - - - +
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Residues in contact with TYR 34 (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 VAL 4.8 0.2 - - - -
9T ALA* 4.6 5.6 - - + -
25T TRP* 3.4 41.7 - + + -
27T PRO* 2.7 32.5 + - - +
29T PRO* 3.7 24.3 - - + +
32T GLN* 3.0 25.6 + - + -
33T VAL* 1.3 77.6 - - - +
35T THR* 1.3 63.1 + - - +
49T CYS 3.3 2.1 - - - +
51T TYR* 2.9 7.8 + - - -
52T THR* 2.8 38.2 + - + +
54T ASP 3.4 18.2 - - - -
55T THR* 4.3 1.1 - - + -
75T VAL* 3.7 13.9 - - + -
76T PHE 3.1 15.5 - - - +
77T SER* 3.5 18.6 - - - -
78T TYR* 4.7 2.0 - - - -
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Residues in contact with THR 35 (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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92L VAL* 6.5 0.4 - - + -
34T TYR* 1.3 70.4 + - - +
36T VAL* 1.3 76.1 + - - +
37T GLN* 5.1 3.4 - - + +
47T SER* 4.3 17.7 - - - +
48T LYS 3.7 7.4 - - - +
49T CYS 3.7 5.8 - - - -
50T PHE* 3.7 8.3 - - + -
51T TYR* 3.0 28.2 + - - -
75T VAL* 3.7 0.7 - - - -
76T PHE* 2.8 37.6 + - + +
78T TYR* 3.8 26.2 - - + +
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Residues in contact with VAL 36 (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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23T LEU* 4.2 17.0 - - + -
25T TRP* 3.6 34.5 - - + -
34T TYR* 5.5 0.2 - - + -
35T THR* 1.3 78.6 - - - +
37T GLN* 1.3 77.4 + - - +
47T SER* 3.3 4.3 - - - -
48T LYS* 2.7 39.9 + - + +
49T CYS* 4.5 2.7 - - + -
57T CYS* 3.7 19.7 - - + -
59T LEU* 4.3 20.0 - - + -
73T ALA* 4.4 0.4 - - + -
74T ARG 3.4 8.3 - - - +
75T VAL* 4.2 8.3 - - + -
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Residues in contact with GLN 37 (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* 3.6 36.3 + - - +
35T THR* 4.3 2.0 + - + +
36T VAL* 1.3 77.6 - - - +
38T ILE* 1.3 61.7 + - - +
45T TRP* 3.7 24.3 + - + +
46T LYS 3.1 7.6 - - - +
47T SER* 3.4 26.7 + - - +
48T LYS* 5.7 0.2 - - - -
73T ALA* 3.0 5.5 - - - +
74T ARG* 2.8 71.7 + - + +
76T PHE* 3.4 17.5 - - + -
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Residues in contact with ILE 38 (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* 4.4 3.6 - - + -
37T GLN* 1.3 77.5 - - - +
39T SER* 1.3 65.2 + - - +
44T ASP 3.9 0.7 - - - +
45T TRP* 3.8 2.7 - - - -
46T LYS* 2.9 42.8 + - + +
48T LYS* 4.4 2.2 - - + -
59T LEU* 4.2 29.8 - - + -
62T GLU* 3.9 32.3 - - + +
63T ILE* 3.8 28.5 - - + -
71T TYR* 4.0 24.0 - - + -
72T LEU 3.3 14.4 - - - +
73T ALA* 4.5 5.6 - - + -
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Residues in contact with SER 39 (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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134H ARG* 2.9 28.8 + - - -
38T ILE* 1.3 77.1 - - - +
40T THR* 1.3 64.7 + - - +
43T GLY 3.9 0.9 - - - -
44T ASP 3.6 17.7 - - - -
45T TRP* 3.2 27.0 - - - -
46T LYS* 5.7 0.7 - - - +
71T TYR* 3.3 9.3 - - - -
72T LEU* 2.9 33.4 + - - +
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Residues in contact with THR 40 (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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134H ARG* 2.9 18.3 + - - -
39T SER* 1.3 76.2 - - - +
41T LYS* 1.3 66.3 + - - +
42T SER* 3.0 4.7 + - - -
43T GLY* 3.0 26.1 + - - +
44T ASP 4.9 0.2 + - - -
69T GLN* 3.8 35.7 + - + +
70T THR 3.5 9.9 - - - +
71T TYR* 3.6 29.2 - - + +
72T LEU* 5.5 0.9 - - - -
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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