Contacts of the strand formed by residues 74 - 80 (chain B) in PDB entry 2Y1Z
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 ARG 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 4.1 3.1 - - - +
70B LEU* 4.0 0.7 - - - +
71B GLU* 2.8 74.9 + - + +
72B LYS 3.6 1.0 - - - -
73B ASP* 1.3 88.6 + - + +
75B PHE* 1.3 57.9 + - - +
76B SER* 3.6 17.8 + - - -
144B THR* 4.5 4.4 - - - +
146B ASN* 3.6 35.6 + - - +
147B GLY 3.5 14.4 - - - +
148B PRO* 4.3 2.7 - - + -
149B ARG* 4.2 7.4 - - - +
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Residues in contact with PHE 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.8 28.0 - - + -
69B ARG 3.6 11.2 - - - -
70B LEU* 4.2 17.9 - - + -
74B ARG* 1.3 75.6 - - - +
76B SER* 1.3 74.2 + - - +
77B VAL* 3.8 27.1 - - + -
98B ILE* 4.5 15.0 - - + -
122B TYR* 5.5 0.4 - - + -
123B ARG 4.2 6.5 - - - -
124B ILE* 4.9 1.6 - - + -
125B PRO* 3.7 34.3 - - + -
128B VAL* 4.0 27.4 - - + -
133B ILE* 5.2 5.8 - - + -
145B VAL 5.4 1.8 - - - -
146B ASN* 3.3 4.4 - - - +
147B GLY 3.0 31.9 + - - +
149B ARG* 4.4 0.6 - - - +
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B MET* 3.5 2.3 - - - -
69B ARG* 2.9 53.7 + - - +
71B GLU* 4.8 0.9 + - - -
74B ARG* 3.6 28.0 + - - -
75B PHE* 1.3 81.1 - - - +
77B VAL* 1.3 65.2 + - - +
78B ASN* 4.3 9.8 + - - -
144B THR* 4.2 9.2 - - - -
145B VAL 3.3 9.9 - - - -
146B ASN* 3.9 2.5 - - - -
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B MET* 4.0 12.8 - - + -
67B GLU 3.5 9.0 - - - +
68B MET* 3.9 13.7 - - + -
75B PHE* 3.8 25.4 - - + -
76B SER* 1.3 79.2 - - - +
78B ASN* 1.3 64.9 + - - +
79B LEU* 4.6 4.2 - - + +
98B ILE* 5.1 3.6 - - + -
122B TYR* 3.8 50.3 - - + +
143B LEU 3.6 1.7 - - - +
144B THR* 3.4 3.5 - - - -
145B VAL* 2.9 41.9 + - + +
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Residues in contact with ASN 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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65B ALA 4.4 0.2 - - - -
66B MET* 3.2 12.5 - - - +
67B GLU* 2.8 65.5 + - + +
69B ARG* 5.2 7.4 + - - +
76B SER* 4.3 11.4 + - - -
77B VAL* 1.3 72.8 - - - +
79B LEU* 1.3 60.3 + - - +
142B VAL* 4.6 9.7 - - + +
143B LEU 3.5 1.3 - - - +
144B THR* 2.5 40.6 + - - +
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Residues in contact with LEU 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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114A ILE* 3.4 31.4 - - + -
116A ARG* 5.9 0.7 - - - +
65B ALA* 3.3 5.8 - - + +
66B MET* 3.6 23.6 - - + -
77B VAL* 4.6 5.2 - - + +
78B ASN* 1.3 77.9 - - - +
80B ASP* 1.3 63.2 + - - +
81B VAL* 3.6 5.8 + - + -
100B VAL* 4.1 13.5 - - + -
118B PHE* 4.5 6.7 - - + -
122B TYR* 3.1 21.1 - - + +
142B VAL* 3.3 10.7 - - - +
143B LEU* 2.7 68.9 + - + +
145B VAL* 5.5 2.5 - - + -
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Residues in contact with ASP 80 (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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82A LYS* 4.7 8.0 + - - +
83A HIS* 2.6 38.0 + - + +
116A ARG* 2.9 29.4 + - - -
64B GLY 5.5 0.2 - - - +
65B ALA* 2.8 20.3 + - + +
79B LEU* 1.3 72.2 - - - +
81B VAL* 1.3 68.5 + - - +
82B LYS* 3.0 24.2 + - - +
118B PHE* 5.5 0.5 - - - -
140B ASP 5.6 0.3 - - - +
141B GLY 3.8 4.6 - - - +
142B VAL* 4.9 6.1 - - + +
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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