Contacts of the strand formed by residues 60 - 66 (chain B) in PDB entry 5HNK
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 ALA 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ARG* 4.8 1.9 + - - -
21B ASN* 3.3 9.9 - - + +
22B LEU 4.6 0.2 - - - -
23B MET* 3.8 22.4 - - + +
55B ALA* 2.9 30.0 + - - +
58B TYR 3.2 4.2 + - - +
59B SER* 1.3 72.4 - - - +
61B ARG* 1.3 60.6 + - - +
62B THR 3.7 18.2 - - - +
63B THR* 3.9 8.8 + - - +
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Residues in contact with ARG 61 (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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20B ARG* 3.3 83.3 + - + +
21B ASN 3.1 6.0 + - - +
59B SER 3.6 4.0 + - - -
60B ALA* 1.3 73.0 - - - +
62B THR* 1.3 68.1 + - - +
143B LEU* 2.9 30.5 + - - +
144B TYR* 3.4 26.2 + - + +
145B ASP* 5.9 0.2 - - - -
289B ALA 5.3 6.5 + - - -
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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
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21B ASN 3.5 1.2 + - - -
22B LEU* 3.5 16.4 - - + -
23B MET 2.9 24.8 + - - -
60B ALA* 3.7 3.6 - - - +
61B ARG* 1.3 87.3 + - - +
63B THR* 1.3 66.6 + - - +
64B ILE* 4.3 5.4 - - + -
120B PRO* 5.5 0.9 - - + -
140B ILE* 5.5 0.2 - - + -
144B TYR* 2.9 37.2 + - - +
288B ILE* 3.6 34.9 + - + +
291B GLN 6.0 1.4 - - - -
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Residues in contact with THR 63 (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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23B MET* 3.3 29.8 - - + +
25B VAL* 4.2 2.7 - - + -
51B ILE* 3.9 18.4 - - + -
55B ALA* 3.6 23.7 - - - +
60B ALA* 3.9 4.7 + - - +
61B ARG 4.4 0.2 - - - -
62B THR* 1.3 77.5 + - - +
64B ILE* 1.3 67.3 + - - +
65B VAL* 4.2 9.4 - - + -
119B PHE* 3.8 23.0 - - + +
120B PRO* 3.4 27.2 - - - +
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Residues in contact with ILE 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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22B LEU* 4.1 15.3 - - + -
23B MET 2.8 9.7 + - - +
24B ILE* 3.3 8.5 - - + +
25B VAL* 2.8 26.3 + - - +
62B THR* 4.3 2.5 - - + -
63B THR* 1.3 77.9 - - - +
65B VAL* 1.3 63.7 + - - +
66B LEU* 4.0 15.3 - - + -
120B PRO* 3.5 7.9 - - + +
122B PHE* 3.7 29.2 - - + -
136B ILE* 4.0 32.8 - - + -
140B ILE* 4.2 10.3 - - + -
285B ILE* 4.4 11.4 - - + -
288B ILE* 4.3 22.7 - - + -
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Residues in contact with VAL 65 (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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25B VAL* 3.8 17.7 - - + -
27B GLY* 4.2 11.7 - - - -
47B TYR* 4.4 4.9 - - - +
51B ILE* 4.2 10.3 - - + -
63B THR* 4.2 9.2 - - + -
64B ILE* 1.3 76.2 - - - +
66B LEU* 1.3 69.9 + - - +
112B PHE* 4.1 19.3 - - + -
115B CYS* 3.7 30.1 - - - -
119B PHE* 4.0 14.1 - - + -
120B PRO 2.9 6.7 + - - +
121B THR* 3.2 12.2 - - + +
122B PHE 2.8 25.8 + - - -
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Residues in contact with LEU 66 (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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24B ILE* 3.6 26.9 - - + -
25B VAL 2.9 14.6 + - - +
26B ASP* 4.2 1.2 - - - +
27B GLY* 2.7 35.0 + - - +
64B ILE* 4.0 5.8 - - + -
65B VAL* 1.3 81.2 - - - +
67B GLY* 1.3 58.3 + - - +
112B PHE* 3.9 4.0 - - - -
122B PHE* 3.5 20.0 - - + -
129B ALA* 3.5 37.7 - - + +
132B MET* 4.0 14.1 - - + -
133B ALA* 3.7 15.7 - - + +
136B ILE* 4.0 19.5 - - + -
156B TRP* 4.5 3.4 - - + -
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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