Contacts of the strand formed by residues 96 - 105 (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 GLU 96 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54B VAL* 4.2 2.8 - - - +
56B ARG* 2.9 48.7 + - - +
73B GLN* 3.7 21.8 - - - +
74B HIS 3.4 4.9 - - - -
75B GLN* 3.9 6.1 - - - +
95B LEU* 1.3 75.6 - - - +
97B GLU* 1.3 61.3 + - - +
98B HIS* 3.8 7.2 - - - +
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Residues in contact with GLU 97 (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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23A ARG* 3.3 30.5 + - - -
54B VAL* 3.6 11.5 - - + +
55B GLN* 3.3 37.0 + - + +
73B GLN* 3.0 3.8 - - - +
74B HIS* 2.7 79.8 + - + +
76B VAL* 3.4 19.8 - - + +
95B LEU 4.0 1.0 - - - -
96B GLU* 1.3 73.0 - - - +
98B HIS* 1.3 63.7 + - - +
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Residues in contact with HIS 98 (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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28B PRO* 3.3 8.4 - - + +
55B GLN* 2.7 48.5 + - - +
56B ARG* 3.5 25.5 + - + -
57B CYS* 3.0 46.2 + - + +
70B PRO* 4.1 18.4 - - + -
72B GLY 3.4 6.5 - - - +
73B GLN* 3.5 32.0 + - + -
74B HIS* 4.9 0.2 - - - -
96B GLU* 3.8 13.0 + - - +
97B GLU* 1.3 80.2 - - - +
99B SER* 1.3 56.0 + - - +
101B CYS* 4.6 0.9 - - - -
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Residues in contact with SER 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B PRO* 3.3 16.3 - - - +
55B GLN* 4.1 8.7 + - - +
72B GLY* 2.7 22.2 + - - -
74B HIS* 4.8 6.3 + - - -
97B GLU 4.1 1.2 + - - -
98B HIS* 1.3 73.7 - - - +
100B GLN* 1.3 80.3 + - - +
1109B GOL 3.2 31.7 - - - -
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Residues in contact with GLN 100 (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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28B PRO* 4.5 4.4 - - - +
57B CYS* 4.0 0.7 - - - -
70B PRO* 3.6 3.6 - - - +
71B THR* 2.8 38.9 + - - +
72B GLY* 3.2 12.0 + - - +
99B SER* 1.3 102.3 + - - +
101B CYS* 1.3 62.3 + - - +
174X LEU* 5.5 10.3 - - - +
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Residues in contact with CYS 101 (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* 3.7 24.8 - - - +
27B GLN* 3.6 2.2 - - - -
28B PRO* 3.3 33.5 - - - +
57B CYS* 2.0 48.5 - - - -
69B VAL 3.4 7.2 - - - +
71B THR* 3.5 9.7 + - - -
98B HIS* 4.6 0.2 - - - -
100B GLN* 1.3 76.4 - - - +
102B GLU* 1.3 65.8 + - - +
173X PRO* 5.0 9.5 - - - +
175X ASP* 5.5 1.2 - - - +
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Residues in contact with GLU 102 (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* 3.7 10.5 - - - -
69B VAL* 2.8 37.9 + - + +
71B THR* 3.4 23.3 - - + +
101B CYS* 1.3 78.6 - - - +
103B CYS* 1.3 63.6 + - - +
104B ARG* 3.1 42.6 + - + +
173X PRO* 6.2 1.3 - - - -
175X ASP* 5.0 11.0 - - - +
199X TYR* 4.7 8.4 + - - -
200X LYS* 4.8 14.4 - - - +
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Residues in contact with CYS 103 (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* 3.7 17.0 - - - +
60B CYS 5.0 0.2 - - - -
61B CYS* 2.0 53.6 - - + -
62B PRO* 3.8 8.1 - - + -
66B LEU* 4.1 15.0 - - + +
67B GLU 3.4 3.8 - - - -
102B GLU* 1.3 73.8 - - - +
104B ARG* 1.3 61.1 + - - +
199X TYR* 3.5 22.1 - - - +
200X LYS* 5.5 1.4 - - - -
202X ILE 5.8 2.0 - - - +
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Residues in contact with ARG 104 (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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66B LEU* 3.9 3.1 - - - -
67B GLU* 2.7 36.7 + - + +
69B VAL* 3.6 29.2 - - + +
70B PRO 5.5 3.3 + - - -
71B THR* 5.1 6.9 - - - +
102B GLU* 3.1 33.0 + - + +
103B CYS* 1.3 73.7 - - - +
105B PRO* 1.3 77.5 - - + +
107B LYS* 4.9 19.4 - - - +
199X TYR* 4.5 9.6 + - + -
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Residues in contact with PRO 105 (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 GLY 3.6 9.4 - - - +
66B LEU* 3.8 7.4 - - + -
67B GLU* 4.8 2.4 - - - +
104B ARG* 1.3 93.0 - - + +
106B LYS* 1.3 68.9 + - - +
107B LYS* 3.5 9.4 + - - +
150X GLU* 5.2 2.5 - - - +
199X TYR* 3.6 47.3 - - + -
224X ARG* 4.9 7.4 - - - +
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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