Contacts of the strand formed by residues 92 - 99 (chain A) in PDB entry 2DFM
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 LEU 92 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 3.8 4.0 - - - +
55A GLN* 2.8 40.2 + - + +
57A LYS* 3.6 36.1 - - + -
83A TYR* 5.1 7.4 - - + -
84A SER 3.9 1.6 - - - -
85A SER* 4.2 20.9 - - - +
90A ASP 3.9 11.2 - - - +
91A GLU* 1.4 84.4 + - - +
93A TYR* 1.3 61.0 + - - +
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Residues in contact with TYR 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 3.2 38.4 - - + +
53A VAL* 3.3 17.9 - - - +
54A LEU* 3.5 28.5 - - + +
55A GLN* 4.8 0.2 - - - -
83A TYR* 3.3 10.4 - - - -
84A SER 2.8 36.7 + - - +
85A SER 4.2 0.4 - - - -
86A GLY* 3.0 38.8 - - - -
87A GLU 4.1 8.6 + - - -
91A GLU* 3.9 21.2 - - + +
92A LEU* 1.3 75.0 - - - +
94A LEU* 1.3 59.6 + - - +
95A ASN* 3.3 4.5 - - - +
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A LYS 3.2 5.4 - - - +
52A LYS* 3.4 0.2 - - - -
53A VAL* 2.8 41.4 + - + +
55A GLN* 4.3 8.7 - - + +
61A ASN* 3.2 39.7 - - + +
64A LEU* 4.2 15.3 - - + -
81A PHE* 4.1 16.8 - - + -
82A PHE 3.7 10.5 - - - +
83A TYR* 3.5 39.3 - - + +
92A LEU 4.2 0.6 + - - -
93A TYR* 1.3 71.4 - - - +
95A ASN* 1.3 62.1 + - - +
96A LEU* 3.7 18.8 - - + +
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Residues in contact with ASN 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.7 13.6 - - + +
51A LYS 3.6 4.0 - - - -
52A LYS* 2.9 38.2 - - - +
81A PHE* 3.1 9.5 - - - +
82A PHE* 2.8 74.3 + - + +
84A SER* 3.7 9.4 - - - -
93A TYR* 3.3 16.8 - - - +
94A LEU* 1.3 74.6 - - - +
96A LEU* 1.3 61.5 + - - +
97A VAL 3.9 0.2 + - - -
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 3.3 5.0 - - - +
50A ILE* 3.4 1.5 - - - -
51A LYS* 3.0 53.9 + - + +
53A VAL* 4.4 5.6 - - + -
63A GLU* 4.3 21.5 - - - +
64A LEU* 4.1 33.9 - - + -
67A MET* 4.5 12.6 - - + -
78A LEU* 3.4 19.5 - - + -
80A TYR 4.0 0.4 - - - -
81A PHE* 4.2 2.5 - - + -
94A LEU* 3.7 27.8 - - + +
95A ASN* 1.3 75.7 - - - +
97A VAL* 1.3 60.3 + - - +
98A LEU* 3.3 13.7 + - + +
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Residues in contact with VAL 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A VAL* 6.5 1.8 - - + -
22A TYR* 6.1 2.5 - - + -
41A LEU* 5.3 5.4 - - + -
48A VAL* 3.8 35.9 - - + -
49A ALA 3.5 3.8 - - - +
50A ILE* 4.1 13.7 - - + +
78A LEU* 3.6 1.4 - - - +
79A ARG* 2.8 41.2 + - + +
80A TYR* 2.9 37.6 + - + +
82A PHE* 4.0 26.7 - - + -
96A LEU* 1.3 71.6 - - - +
98A LEU* 1.3 55.7 + - - +
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Residues in contact with LEU 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.3 7.3 - - - +
49A ALA* 2.7 40.7 + - + +
51A LYS* 5.2 18.2 - - + +
67A MET* 4.5 16.6 - - - -
76A VAL* 4.0 19.5 - - + -
77A ARG 3.5 7.4 - - - +
78A LEU* 3.3 43.7 - - + +
79A ARG* 4.7 2.0 - - - -
96A LEU* 4.1 15.5 - - + +
97A VAL* 1.3 74.9 - - - +
99A GLU* 1.3 65.0 + - - +
165A CYS* 6.0 1.6 - - + -
166A ASP* 5.9 4.3 - - - +
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Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A GLU* 5.4 3.5 - - - +
47A LEU 4.6 5.8 - - - +
48A VAL* 4.6 2.5 - - - +
49A ALA* 4.3 4.6 - - - +
76A VAL* 3.9 19.0 - - + +
77A ARG* 3.4 34.4 + - + +
79A ARG* 4.6 21.8 + - - +
98A LEU* 1.3 80.4 - - - +
100A TYR* 1.3 69.0 + - - +
101A VAL* 3.9 8.0 + - + +
154A LEU* 4.9 2.9 - - - +
163A LYS* 3.2 31.7 + - - +
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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