Contacts of the strand formed by residues 19 - 35 (chain B) in PDB entry 1XWD
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 PHE 19 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B GLU* 3.4 2.3 - - - +
14B LYS* 2.7 42.6 + - + +
17B CYS* 3.2 36.1 - - + -
18B ARG* 1.3 79.1 - - - +
20B CYS* 1.3 74.3 + - - +
21B ILE* 4.3 16.4 - - + -
63B VAL* 5.2 0.9 - - + -
64B PRO* 3.6 25.8 - - + -
65B GLY 3.4 24.0 - - - -
66B CYS* 4.3 5.2 - - + -
104B CYS* 5.0 0.2 - - - -
106B PHE* 3.6 9.0 - - - -
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Residues in contact with CYS 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 4.3 8.7 - - + -
12B ILE 3.0 12.8 - - - +
13B GLU* 2.9 31.6 - - - -
19B PHE* 1.3 81.6 - - - +
21B ILE* 1.3 70.9 + - - +
103B TYR 4.5 2.5 - - - -
104B CYS* 2.0 53.1 - - + -
106B PHE* 4.3 0.2 - - - -
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B ALA* 3.6 2.7 - - - -
12B ILE* 2.8 45.9 + - + +
19B PHE* 4.3 10.8 - - + -
20B CYS* 1.3 79.8 - - - +
22B SER* 1.3 62.6 + - - +
23B ILE* 4.0 22.6 + - + -
61B VAL* 4.9 1.8 - - + -
62B ARG 4.0 20.9 - - - +
63B VAL* 4.0 13.4 - - + +
64B PRO* 3.6 33.7 - - + -
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Residues in contact with SER 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR* 3.9 21.3 - - - +
10B ILE 3.7 5.0 + - - -
11B ALA* 4.7 7.2 - - - +
21B ILE* 1.3 75.1 - - - +
23B ILE* 1.3 64.9 + - - +
102B SER* 5.5 3.1 - - - -
113B NAG 4.2 16.5 - - - +
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Residues in contact with ILE 23 (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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9B THR* 3.5 2.3 - - - -
10B ILE* 2.9 44.0 + - + +
12B ILE* 2.9 33.9 - - + -
21B ILE* 4.2 13.7 - - + -
22B SER* 1.3 81.2 - - - +
24B ASN* 1.3 77.0 + - - +
25B THR 3.7 0.2 + - - -
61B VAL* 3.4 33.0 - - + -
76B TYR* 3.8 24.9 - - + +
113B NAG 5.2 1.6 - - - -
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Residues in contact with ASN 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 5.9 5.8 - - + +
8B ILE 3.6 5.2 - - - +
9B THR* 3.1 26.4 + - - +
23B ILE* 1.3 79.2 - - - +
25B THR* 1.3 61.2 + - - +
76B TYR* 5.0 1.7 + - - -
112B NAG 5.7 3.4 + - - -
113B NAG 1.5 67.8 + - + +
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Residues in contact with THR 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASN* 3.3 10.2 - - - +
8B ILE* 2.9 33.8 + - + +
10B ILE* 3.7 41.5 - - + -
23B ILE* 4.8 0.7 - - - -
24B ASN* 1.3 73.9 - - - +
26B THR* 1.3 72.1 + - - +
27B TRP* 4.0 13.7 - - + +
59B GLU* 5.0 0.4 + - - -
76B TYR* 4.1 13.9 - - + -
78B VAL* 3.1 28.4 - - - +
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Residues in contact with THR 26 (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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5B LEU* 4.2 22.2 - - + -
6B THR 3.3 13.2 - - - +
7B ASN* 3.4 19.9 + - - +
25B THR* 1.3 85.5 + - - +
27B TRP* 1.3 72.5 + - - +
78B VAL* 4.0 8.0 - - - +
79B ALA* 3.2 28.2 + - - +
112B NAG 4.6 10.8 - - + +
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Residues in contact with TRP 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 3.3 35.7 - - + +
37A TYR* 3.8 1.3 - - - -
38A PRO* 3.2 26.6 - - + +
53A VAL* 3.6 39.0 - - + -
5B LEU* 3.2 6.8 - - - -
6B THR* 2.6 44.5 + - - -
8B ILE* 3.8 17.5 - - + +
25B THR* 4.0 14.1 - - + -
26B THR* 1.3 84.7 + - - +
28B CYS* 1.3 64.6 + - - +
53B PHE* 4.0 17.9 - + + -
56B LEU* 3.9 11.9 - - + -
77B PRO* 2.8 51.1 + - + -
79B ALA* 3.6 24.5 - - + -
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Residues in contact with CYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.3 2.9 - - - +
36A ALA* 3.1 31.2 + - + +
4B GLU 3.9 0.7 - - - -
6B THR* 4.3 0.6 + - - -
8B ILE* 5.7 1.4 - - - +
27B TRP* 1.3 83.8 - - - +
29B ALA* 1.3 66.1 + - - +
51B CYS* 3.9 12.6 - - - -
52B THR* 3.4 27.1 - - - -
53B PHE* 3.5 10.1 - - - -
79B ALA* 4.0 8.3 - - - -
82B CYS* 2.1 46.0 - - - -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A PHE* 4.0 11.7 - - + -
34A SER 3.5 9.9 - - - -
35A ARG* 3.8 12.8 - - + -
4B GLU* 3.1 36.0 + - - +
6B THR* 3.8 19.8 - - + +
8B ILE* 5.9 2.2 - - + -
28B CYS* 1.3 77.4 - - - +
30B GLY* 1.3 58.5 + - - +
51B CYS* 3.6 7.7 - - - -
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Residues in contact with GLY 30 (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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33A PHE* 3.3 15.2 - - - -
34A SER* 3.0 36.6 + - - +
3B CYS* 3.8 10.3 - - - -
4B GLU* 4.7 4.7 - - - -
29B ALA* 1.3 77.4 - - - +
31B TYR* 1.3 70.4 + - - -
51B CYS* 4.8 0.2 - - - -
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Residues in contact with TYR 31 (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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3A ASP 6.2 0.2 - - - -
5A GLN* 5.2 0.3 + - - -
7A CYS* 3.9 29.6 - - + -
31A CYS* 3.9 17.5 - - + -
32A CYS* 3.3 19.7 - - - -
33A PHE* 3.7 37.0 - + + +
3B CYS* 3.2 22.4 + - - +
30B GLY* 1.3 77.9 - - - -
32B CYS* 1.3 72.7 + - - +
84B CYS* 3.6 2.1 - - - -
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Residues in contact with CYS 32 (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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7A CYS* 4.2 1.6 - - - -
30A GLY 3.7 0.2 - - - +
31A CYS* 3.3 21.5 - - - -
32A CYS* 3.3 12.6 + - - +
34A SER* 4.4 3.1 - - - +
3B CYS* 3.8 2.5 - - - -
31B TYR* 1.3 80.2 - - - +
33B TYR* 1.3 64.3 + - - +
34B THR* 3.8 3.3 + - - +
49B LYS 3.8 19.1 - - - +
50B THR* 4.7 0.4 - - - -
51B CYS* 3.6 29.6 - - - +
84B CYS* 2.0 51.1 - - + -
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Residues in contact with TYR 33 (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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7A CYS* 4.1 3.2 - - - -
8A PRO* 5.4 9.4 - - + -
29A MET* 3.1 34.0 - - + +
30A GLY* 3.3 35.9 - - - -
31A CYS* 3.8 12.6 - - - -
32B CYS* 1.3 77.0 - - - +
34B THR* 1.3 75.9 + - - +
35B ARG* 3.0 40.0 + - - -
49B LYS* 4.6 10.0 + - - +
84B CYS* 5.0 1.2 - - - +
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Residues in contact with THR 34 (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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29A MET* 3.3 1.2 - - - -
30A GLY 2.9 31.2 + - - +
32A CYS* 4.6 3.5 + - - +
58A THR 5.1 0.8 + - - +
59A CYS* 4.2 9.9 - - - -
60A CYS* 3.3 32.2 + - - +
32B CYS 4.3 4.7 + - - +
33B TYR* 1.3 90.4 - - - +
35B ARG* 1.3 63.4 + - - +
47B ILE 5.1 1.6 - - - +
48B GLN* 4.0 16.8 - - + -
49B LYS 3.6 33.7 - - - +
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Residues in contact with ARG 35 (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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17A PHE* 5.8 4.2 - - - -
27A GLN* 4.4 8.3 + - - +
28A CYS 3.2 6.1 - - - +
29A MET* 3.7 23.1 - - + +
60A CYS 4.0 6.6 - - - +
61A VAL* 5.8 0.3 - - - +
33B TYR* 3.0 35.5 + - - -
34B THR* 1.3 77.1 - - - +
36B ASP* 1.3 60.5 + - - +
37B LEU* 4.1 12.2 + - + +
46B LYS* 6.0 2.1 - - - +
47B ILE 5.1 9.0 + - - +
48B GLN* 5.3 6.4 + - - +
403B SO4 2.9 39.9 + - - +
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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