Contacts of the helix formed by residues 57 - 70 (chain B) in PDB entry 4K8T
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 GLY 57 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ASN 3.4 23.8 - - - -
10B ALA* 5.2 0.4 - - - -
11B ILE* 3.6 7.3 + - - +
56B GLY* 1.3 68.0 - - - +
58B SER* 1.3 68.5 + - - -
59B ALA 3.4 2.2 - - - -
60B GLY* 3.2 4.2 + - - -
61B ASN* 2.9 28.4 + - - -
88B PHE* 5.2 0.2 - - - -
401B ADN 2.9 22.2 + - - -
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Residues in contact with SER 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLY* 1.3 71.8 - - - +
59B ALA* 1.3 59.4 + - - +
61B ASN* 3.3 4.0 + - - +
62B THR* 3.0 28.4 + - - -
152B TYR* 4.9 3.0 + - - -
154B GLU* 3.2 20.9 + - - +
156B TYR* 4.0 15.1 - - - -
184B THR* 4.8 10.0 - - - +
186B SER* 5.9 0.7 - - - -
276B ASP* 2.2 38.4 + - - -
401B ADN 3.2 21.6 + - - -
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Residues in contact with ALA 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 2.8 31.7 + - - +
7B VAL 3.4 33.9 - - - +
8B GLY* 3.8 2.9 - - - +
58B SER* 1.3 69.7 - - - +
60B GLY* 1.3 60.3 + - - +
62B THR* 3.3 8.0 + - - -
63B ALA* 2.9 18.2 + - - +
75B TYR* 3.8 1.6 - - + -
152B TYR* 4.5 7.9 - - + -
154B GLU* 2.7 24.2 + - + +
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Residues in contact with GLY 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B GLY 4.2 2.2 - - - -
57B GLY 3.2 8.1 + - - -
59B ALA* 1.3 76.7 - - - +
61B ASN* 1.3 56.9 + - - +
63B ALA* 3.2 4.7 + - - +
64B ALA* 2.9 28.9 + - - +
75B TYR* 3.3 26.2 - - - -
88B PHE* 4.9 0.2 - - - -
92B ILE* 4.0 13.5 - - - +
313B ARG* 3.8 13.0 - - - -
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Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER 3.7 0.2 - - - +
56B GLY* 3.5 10.0 - - - -
57B GLY 2.9 15.7 + - - +
58B SER 3.4 6.3 - - - +
60B GLY* 1.3 73.5 - - - +
62B THR* 1.3 57.8 + - - +
64B ALA* 3.3 2.6 + - - +
65B GLY* 2.9 25.6 + - - -
276B ASP* 3.0 29.0 + - + +
277B LEU* 4.1 7.5 - - + +
280B SER* 3.7 1.7 + - - -
312B PRO* 3.3 25.6 + - - +
313B ARG* 2.8 38.8 + - - +
314B PRO* 5.9 0.2 - - - +
401B ADN 3.1 25.3 + - - -
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Residues in contact with THR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.9 9.4 - - + -
58B SER 3.0 15.1 + - - -
59B ALA 3.6 7.0 - - - -
60B GLY 3.2 0.4 - - - -
61B ASN* 1.3 76.3 - - - +
63B ALA* 1.3 62.0 + - - +
65B GLY 3.2 0.2 + - - -
66B VAL* 3.0 15.9 + - + +
152B TYR* 3.8 31.1 + - + -
276B ASP* 2.7 26.7 + - - +
279B ALA* 3.9 6.5 - - + -
280B SER* 2.7 36.7 + - - +
283B LEU* 4.5 5.8 - - + -
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B THR* 3.5 26.2 - - + +
59B ALA 2.9 7.0 + - - +
60B GLY 3.5 7.6 - - - +
62B THR* 1.3 75.1 - - - +
64B ALA* 1.3 63.6 + - - +
65B GLY 3.2 0.3 + - - -
66B VAL* 3.2 6.4 + - - +
67B ALA* 3.0 19.9 + - - +
73B ALA* 3.6 13.8 - - + +
74B ALA 4.1 13.2 - - - +
75B TYR* 4.4 5.2 - - + -
92B ILE* 4.7 1.1 - - + -
97B VAL* 3.9 20.0 - - + -
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Residues in contact with ALA 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60B GLY 2.9 17.1 + - - +
61B ASN 3.6 4.9 - - - +
63B ALA* 1.3 76.1 - - - +
65B GLY* 1.3 57.0 + - - +
67B ALA 3.4 0.5 + - - -
68B ASN* 2.9 27.8 + - - +
92B ILE* 5.4 1.6 - - + -
95B GLN* 3.4 30.3 - - + +
97B VAL* 4.1 6.2 - - + +
313B ARG* 3.6 33.0 - - + +
314B PRO* 6.4 0.4 - - + -
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Residues in contact with GLY 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ASN 2.9 12.3 + - - -
63B ALA 3.1 0.4 - - - -
64B ALA* 1.3 74.3 - - - +
66B VAL* 1.3 64.2 + - - +
68B ASN* 3.6 1.5 + - - -
69B LEU* 3.1 29.1 + - - +
277B LEU* 3.8 14.8 - - - -
280B SER* 3.3 22.2 - - - -
314B PRO* 5.6 2.2 - - - +
318B LEU* 3.6 7.4 - - - +
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Residues in contact with VAL 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 5.2 1.6 - - + -
4B VAL* 4.1 36.6 - - + -
62B THR* 3.0 17.3 + - + +
63B ALA* 3.5 7.6 - - - +
65B GLY* 1.3 77.2 - - - +
67B ALA* 1.3 60.1 + - - +
69B LEU* 3.3 7.4 + - - +
70B GLY 3.2 4.9 + - - -
71B GLY* 3.0 39.7 + - - -
72B LYS 4.4 1.3 - - - +
73B ALA* 4.0 16.8 - - + -
280B SER* 3.6 26.2 - - - +
283B LEU* 4.8 1.6 - - + -
284B TYR* 4.3 8.9 - - + +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ALA 3.0 12.5 + - - +
64B ALA 3.6 7.2 - - - +
66B VAL* 1.3 73.7 - - - +
68B ASN* 1.3 67.1 + - - +
70B GLY* 2.9 15.8 + - - -
71B GLY 3.6 13.8 - - - +
73B ALA* 4.4 4.0 - - + +
95B GLN* 3.4 26.2 - - + +
96B GLY 4.5 6.5 - - - +
97B VAL* 3.9 15.7 - - + -
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ALA 2.9 18.7 + - - +
65B GLY* 3.6 6.7 - - - +
67B ALA* 1.3 72.2 - - - +
69B LEU* 1.3 62.4 + - - +
70B GLY* 3.2 1.6 + - - -
95B GLN* 3.5 23.1 + - - +
314B PRO* 3.6 19.8 + - - +
316B THR 3.0 20.6 + - - -
317B SER* 3.6 6.4 + - - -
318B LEU* 2.7 41.2 + - + +
319B SER* 3.7 13.3 + - - -
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY 3.1 21.6 + - - +
66B VAL 3.6 5.4 - - - +
67B ALA 3.2 0.2 - - - -
68B ASN* 1.3 75.0 - - - +
70B GLY* 1.3 56.8 + - - +
71B GLY 3.7 0.4 - - - -
280B SER 3.6 10.5 - - - +
281B GLY* 3.6 32.1 - - - +
284B TYR* 3.5 43.9 + - + -
298B LEU* 4.3 8.7 - - + +
301B LEU* 5.9 2.2 - - + -
302B ALA* 4.8 4.7 - - + -
318B LEU* 3.8 35.9 - - + +
319B SER* 3.3 22.1 - - - +
322B ALA* 4.2 15.3 - - + -
328B ILE 5.6 0.2 - - - +
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Residues in contact with GLY 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA 2.9 11.8 + - - -
68B ASN 3.2 1.9 - - - -
69B LEU* 1.3 78.6 - - - +
71B GLY* 1.3 64.0 + - - +
72B LYS* 5.1 5.5 - - - +
284B TYR* 3.9 6.5 - - - -
319B SER* 5.2 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