Contacts of the strand formed by residues 95 - 104 (chain A) in PDB entry 2XKL
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 CYS 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A THR* 3.8 7.0 - - + -
88A ILE 3.3 3.4 - - - -
89A ARG* 3.9 14.8 - - - -
94A VAL* 1.3 79.9 - - - +
96A VAL* 1.3 63.1 + - - +
97A PRO* 3.5 9.0 - - + +
185A CYS* 2.1 50.3 - - + -
186A PRO* 4.2 10.8 - - + -
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Residues in contact with VAL 96 (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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87A THR* 3.6 1.1 - - - -
88A ILE* 2.8 50.5 + - + +
90A THR* 4.0 19.7 - - - +
94A VAL* 4.8 7.6 - - + -
95A CYS* 1.3 74.4 - - - +
97A PRO* 1.3 64.5 - - + +
98A ARG* 3.6 39.3 - - - +
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Residues in contact with PRO 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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86A ALA 3.4 9.6 - - - +
87A THR* 3.8 13.7 - - + +
95A CYS* 3.5 10.5 - - + +
96A VAL* 1.3 89.5 - - + +
98A ARG* 1.3 74.1 + - - +
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Residues in contact with ARG 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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84A LEU 3.7 0.6 - - - +
85A ARG* 3.4 2.6 - - - +
86A ALA* 2.7 49.1 + - + +
88A ILE* 4.1 8.1 - - + +
96A VAL* 3.6 29.9 - - - +
97A PRO* 1.3 85.7 + - - +
99A LYS* 1.3 59.1 + - - +
100A TRP* 3.2 48.8 - - + +
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Residues in contact with LYS 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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83A GLN* 3.1 39.4 + - + +
84A LEU 3.3 2.9 - - - +
85A ARG* 3.7 38.4 - - + +
98A ARG* 1.3 72.5 - - - +
100A TRP* 1.3 69.6 + - - +
101A THR* 3.5 21.3 + - - +
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Residues in contact with TRP 100 (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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63A PHE* 5.5 2.5 - + - -
69A ILE* 4.8 4.9 - - + -
82A LEU 3.7 0.9 - - - +
83A GLN* 3.2 4.9 - - - +
84A LEU* 2.8 48.0 + - + +
86A ALA* 4.3 17.7 - - + -
88A ILE* 3.7 24.2 - - + -
98A ARG* 3.2 35.2 - - + +
99A LYS* 1.3 80.2 - - - +
101A THR* 1.3 62.7 + - - +
102A TYR* 3.6 33.0 - + + +
1190A GOL 3.9 26.5 + - - -
1191A POL 3.6 32.8 - - + -
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Residues in contact with THR 101 (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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26A HIS* 3.3 44.2 + - + +
27A SER* 4.7 2.4 + - - -
81A GLN* 4.1 11.4 + - - -
82A LEU 3.4 2.5 - - - -
83A GLN* 3.6 20.9 - - - +
99A LYS* 3.5 24.7 - - - +
100A TRP* 1.3 74.7 - - - +
102A TYR* 1.3 65.1 + - - +
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Residues in contact with TYR 102 (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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26A HIS* 3.8 6.5 - - - -
27A SER* 3.3 23.6 - - - +
29A LEU* 3.4 42.6 - - + -
81A GLN* 3.4 12.0 - - - +
82A LEU* 2.8 43.0 + - + +
84A LEU* 3.9 22.0 - - + -
100A TRP* 3.6 33.3 - - + +
101A THR* 1.3 77.5 - - - +
103A ARG* 1.3 64.6 + - - +
138A GLU* 3.5 20.0 - - - -
1190A GOL 2.8 36.3 + - - -
1191A POL 3.7 8.2 + - - -
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Residues in contact with ARG 103 (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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24A PRO 3.4 21.5 + - - -
25A GLU* 3.4 25.9 + - - +
26A HIS* 2.8 41.6 + - + +
27A SER 2.8 10.5 + - - +
28A GLN* 3.3 37.7 - - + +
29A LEU* 2.9 25.8 + - - -
80A ARG* 3.8 10.5 - - + +
81A GLN* 4.7 3.4 - - + +
102A TYR* 1.3 75.1 - - - +
104A LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 104 (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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28A GLN* 4.7 1.5 - - - +
29A LEU* 3.6 24.7 - - + +
30A THR* 5.8 0.4 - - - -
31A ALA 5.9 2.5 - - - +
43A HIS* 5.8 3.8 - - + +
80A ARG* 2.9 56.4 + - - +
81A GLN 4.3 12.8 - - - +
82A LEU* 4.0 42.4 - - + +
102A TYR 4.0 0.2 + - - -
103A ARG* 1.3 83.5 - - - +
105A THR* 1.3 64.7 + - - +
106A GLU* 3.7 1.4 + - - +
136A LEU* 6.4 0.2 - - + -
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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