Contacts of the strand formed by residues 66 - 75 (chain B) in PDB entry 2XAC
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 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B CYS* 3.6 21.0 - - + +
62B PRO* 3.7 38.1 - - + -
63B ASP* 2.9 25.2 + - - +
64B ASP* 3.9 0.5 - - - +
65B GLY* 1.3 79.4 - - - +
67B GLU* 1.3 59.5 + - - +
103B CYS* 4.1 13.0 - - + +
104B ARG 3.4 4.9 - - - +
105B PRO* 3.8 21.1 - - + -
106B LYS* 3.9 8.2 - - - -
199X TYR* 4.0 17.5 - - + +
202X ILE* 4.1 17.7 - - + +
224X ARG* 3.8 21.5 - - - +
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Residues in contact with GLU 67 (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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61B CYS* 3.5 4.0 - - - -
66B LEU* 1.3 73.9 - - - +
68B CYS* 1.3 58.8 + - - +
69B VAL* 3.4 27.4 + - + +
103B CYS* 3.4 2.4 - - - -
104B ARG* 2.7 43.5 + - + +
105B PRO 4.8 1.7 - - - +
106B LYS* 3.2 48.6 + - + +
107B LYS* 4.9 15.2 + - - +
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Residues in contact with CYS 68 (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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26B CYS* 2.0 49.4 - - + -
57B CYS* 4.0 13.2 - - - +
58B GLY* 3.4 30.1 - - - -
59B GLY 4.4 12.1 - - - +
61B CYS* 3.6 12.7 - - - +
67B GLU* 1.3 71.6 - - - +
69B VAL* 1.3 60.5 + - - +
70B PRO* 4.6 0.7 - - - +
102B GLU 3.8 0.2 - - - -
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Residues in contact with VAL 69 (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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57B CYS* 3.8 4.9 - - - -
67B GLU* 3.4 35.9 + - + +
68B CYS* 1.3 75.3 - - - +
70B PRO* 1.4 73.3 - - + +
101B CYS* 3.4 2.6 - - - +
102B GLU* 2.8 43.3 + - + +
104B ARG* 3.6 38.6 - - + +
107B LYS* 6.2 1.6 - - - +
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Residues in contact with PRO 70 (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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57B CYS* 3.3 26.7 - - + -
68B CYS 4.6 0.9 - - - +
69B VAL* 1.4 98.4 - - + +
71B THR* 1.3 62.6 + - - +
72B GLY 4.5 6.1 - - - +
73B GLN* 4.1 19.7 - - + +
98B HIS* 4.1 24.7 - - + -
100B GLN 3.6 2.2 - - - +
104B ARG* 5.5 3.8 + - - -
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Residues in contact with THR 71 (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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69B VAL* 5.6 0.2 - - + -
70B PRO* 1.3 76.3 - - - +
72B GLY* 1.3 57.3 + - - +
100B GLN* 2.8 32.4 + - - +
101B CYS* 3.3 5.2 + - - +
102B GLU* 3.4 45.1 - - + +
104B ARG* 5.1 7.4 - - - +
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Residues in contact with GLY 72 (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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70B PRO* 3.6 2.0 - - - +
71B THR* 1.3 80.0 - - - +
73B GLN* 1.3 60.3 + - - +
98B HIS* 3.4 3.6 - - - +
99B SER* 2.7 43.2 + - - -
100B GLN* 3.2 10.9 + - - +
1109B GOL 4.3 9.4 - - - -
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Residues in contact with GLN 73 (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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70B PRO* 4.1 16.2 - - + +
72B GLY* 1.3 75.3 - - - +
74B HIS* 1.3 64.4 + - - +
75B GLN* 4.2 10.0 + - - -
96B GLU* 3.7 18.8 - - - +
97B GLU 3.0 14.8 - - - +
98B HIS* 3.5 26.4 + - + +
99B SER 4.3 1.1 - - - +
1109B GOL 3.3 18.0 + - - -
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Residues in contact with HIS 74 (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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55B GLN* 5.0 2.2 - - - -
73B GLN* 1.3 78.0 - - - +
75B GLN* 1.3 83.5 + - - +
76B VAL* 3.8 8.6 - - + +
96B GLU* 3.4 5.4 - - - +
97B GLU* 2.7 82.7 + - + +
98B HIS 4.7 5.2 - - - -
99B SER* 4.8 5.9 - - - -
1109B GOL 3.0 25.2 + - - +
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Residues in contact with GLN 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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73B GLN* 4.2 7.3 + - - -
74B HIS* 1.3 91.2 + - - +
76B VAL* 1.3 60.7 + - - +
77B ARG* 4.0 4.7 + - + +
94B SER* 4.0 20.0 - - - +
95B LEU* 3.0 32.6 + - - +
96B GLU* 3.9 13.7 - - - +
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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