Contacts of the strand formed by residues 74 - 79 (chain B) in PDB entry 5HKE
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 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PHE* 3.8 14.4 - - - -
67B ALA 3.4 9.6 - - - -
68B ILE* 3.8 11.2 - - - +
72B GLY 3.9 1.0 + - - -
73B LEU* 1.3 74.8 - - - +
75B MET* 1.3 60.7 + - - +
107B LEU* 4.0 2.2 - - - -
143B ILE* 3.2 9.0 - - - +
144B ALA 2.7 38.0 + - - -
280B LEU* 4.5 1.2 - - - +
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Residues in contact with MET 75 (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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14B PHE* 3.6 3.9 - - - -
66B ASP* 3.2 3.6 - - - +
67B ALA 3.0 32.7 + - - +
74B GLY* 1.3 75.5 - - - +
76B ALA* 1.3 63.1 + - - +
102B PHE* 3.5 53.2 - - + +
103B ILE* 3.8 25.6 - - + +
106B ILE* 3.8 25.6 - - + -
107B LEU* 3.9 15.4 - - + +
141B TRP* 3.7 21.1 - - + -
142B LEU 3.2 5.8 - - - +
143B ILE* 3.7 22.0 - - + -
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Residues in contact with ALA 76 (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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4B ALA* 4.7 7.6 - - + -
14B PHE* 3.7 17.7 - - + -
16B ARG* 4.1 8.3 - - + +
65B PHE 3.6 4.5 - - - -
66B ASP* 3.8 13.7 - - + -
75B MET* 1.3 75.4 - - - +
77B GLY* 1.3 59.5 + - - +
78B LEU* 3.6 17.8 - - + +
103B ILE* 4.7 0.4 - - - -
141B TRP* 3.1 11.9 - - - -
142B LEU* 2.9 33.0 + - + +
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Residues in contact with GLY 77 (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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2B OCS 3.9 1.0 + - - -
16B ARG* 2.8 28.2 + - - -
64B TYR 6.0 0.2 - - - -
65B PHE* 3.0 15.8 + - - +
76B ALA* 1.3 71.8 - - - +
78B LEU* 1.3 54.3 + - - -
103B ILE* 4.3 4.1 - - - +
139B LEU* 4.2 14.4 - - - +
140B HIS 3.5 1.1 - - - -
141B TRP* 3.4 23.9 - - - -
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Residues in contact with LEU 78 (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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2B OCS 3.2 26.0 - - + +
4B ALA* 3.7 23.3 - - + +
16B ARG* 3.7 6.5 - - - +
76B ALA* 3.6 29.4 - - + +
77B GLY* 1.3 80.2 - - - +
79B ASN* 1.3 67.8 + - - +
139B LEU* 3.2 6.6 - - - +
140B HIS* 2.8 36.8 + - + +
142B LEU 4.7 0.7 - - - +
169B LEU* 3.5 31.9 - - + +
170B THR 3.3 26.9 - - - +
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Residues in contact with ASN 79 (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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2B OCS 2.8 28.5 + - - +
19B ASP 4.3 2.4 + - - -
20B LEU* 3.9 24.0 - - - +
78B LEU* 1.3 72.2 - - - +
80B PHE* 1.3 60.2 + - - +
81B PRO* 3.7 10.3 - - + -
137B ALA* 4.1 11.4 - - - +
138B GLY 3.5 7.1 - - - +
139B LEU* 3.7 14.1 - - - +
140B HIS* 3.8 1.2 - - - -
171B ASN* 2.8 38.8 + - - +
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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