Contacts of the strand formed by residues 63 - 70 (chain B) in PDB entry 1XIW
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 SER 63 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 3.4 8.4 - - - +
1B MET* 2.7 44.1 + - - +
2B LYS* 5.0 0.2 - - - -
3B ILE* 3.9 19.5 - - - -
51B ARG* 3.1 21.3 - - - +
52B CYS* 3.2 17.6 + - - -
62B GLU* 1.3 78.5 + - - +
64B THR* 1.3 64.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ASN* 2.7 16.3 + - - +
89A PHE* 3.3 22.4 - - + -
90A TYR* 2.9 27.4 + - - +
1B MET 5.6 0.2 - - - +
3B ILE* 4.1 3.8 + - - -
49B ILE* 3.6 22.0 - - + -
50B TYR 3.3 13.9 - - - +
51B ARG* 2.8 39.8 + - - +
62B GLU* 3.9 4.2 + - - -
63B SER* 1.3 74.3 + - - +
65B VAL* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A TYR* 4.4 11.7 - - + -
89A PHE* 4.4 3.6 - - - -
90A TYR* 3.3 12.6 - - + +
92A TYR* 4.0 26.2 - - + +
3B ILE* 3.9 30.5 - - + +
5B ILE* 4.1 22.4 - - + -
14B VAL* 4.6 0.7 - - + -
49B ILE* 3.4 1.9 - - - +
50B TYR* 2.8 52.9 + - + +
64B THR* 1.3 75.2 - - - +
66B GLN* 1.3 65.1 + - - +
67B VAL* 4.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO* 3.4 16.9 - - - +
15A TYR* 2.8 48.9 + - + +
17A VAL* 4.3 6.9 - - - +
89A PHE* 3.5 16.1 - - + -
90A TYR 2.7 16.1 + - - +
91A LEU* 3.4 23.3 - - + +
92A TYR 2.7 32.2 + - - -
48B GLY 3.2 12.6 - - - +
49B ILE* 3.9 9.0 - - + +
65B VAL* 1.3 72.3 - - - +
67B VAL* 1.3 61.6 + - - +
68B HIS* 5.2 4.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.6 6.7 - - + +
5B ILE* 3.6 33.4 - - + -
12B VAL* 4.8 1.3 - - + -
39B LEU* 4.2 17.0 - - + -
46B PRO 3.9 7.2 - - - +
47B ARG* 3.2 5.4 - - - +
48B GLY 2.8 27.4 + - - +
50B TYR* 4.0 26.7 - - + -
65B VAL* 4.5 4.5 - - + -
66B GLN* 1.3 78.8 - - - +
68B HIS* 1.3 64.3 + - - +
69B TYR* 3.5 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.6 44.3 + - + +
19A ILE* 3.9 15.7 - - + +
91A LEU* 4.4 14.4 - - + -
92A TYR 2.9 12.6 + - - +
93A LEU* 3.7 15.0 - - + +
94A ARG 3.1 24.1 + - - +
47B ARG* 3.7 42.9 + - + +
66B GLN* 5.2 4.3 + - + -
67B VAL* 1.3 77.7 + - - +
69B TYR* 1.3 68.7 + - - +
70B ARG* 4.4 0.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A TYR* 3.7 17.3 - + - -
94A ARG* 3.2 29.6 - - + -
5B ILE* 4.1 1.6 - - - +
7B GLU* 2.6 42.4 + - - +
12B VAL* 3.6 31.3 - - + +
42B ARG* 4.1 17.7 - - + +
45B ASP* 3.2 12.1 - - - +
46B PRO* 3.1 35.6 + - + +
47B ARG* 2.9 24.6 + - - +
67B VAL* 3.5 28.9 - - + -
68B HIS* 1.3 75.3 - - - +
70B ARG* 1.3 59.0 + - - +
71B MET* 4.1 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A ILE* 3.4 62.8 + - + +
20A SER* 5.1 0.2 - - - +
21A GLY 4.8 8.3 + - - +
94A ARG 3.0 7.3 + - - -
95A ALA* 3.4 4.6 - - + -
96A ARG 2.7 60.5 + - - +
97A VAL* 3.5 11.9 - - - +
98A CYS 4.5 1.0 + - - -
101A CYS* 3.1 41.2 - - - +
102A MET 5.1 1.6 - - - +
45B ASP* 3.5 6.5 - - - +
47B ARG* 3.7 16.8 - - - +
68B HIS* 4.4 2.0 - - - +
69B TYR* 1.3 74.8 - - - +
71B MET* 1.3 60.8 + - - +
72B CYS 3.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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