Contacts of the strand formed by residues 35 - 43 (chain A) in PDB entry 6U6V
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 THR 35 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 1.3 78.0 - - - +
36A PHE* 1.3 65.2 + - - +
68A HIS* 6.0 1.6 - - - -
69A HIS 3.7 13.2 - - - +
70A GLY* 5.0 2.7 - - - -
118A GLU* 3.7 1.0 - - - -
119A ILE* 2.8 60.4 + - - +
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Residues in contact with PHE 36 (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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1A PHE* 3.8 31.2 - + - -
24A LEU* 5.1 4.0 - - + -
34A VAL* 3.5 26.0 - - + -
35A THR* 1.3 76.3 - - - +
37A TYR* 1.3 59.2 + - - +
38A LYS* 3.9 24.2 - - + -
67A LEU 3.8 0.7 - - - +
68A HIS* 3.3 6.9 - - - +
69A HIS* 2.9 54.2 + + - +
71A GLY* 4.0 20.0 - - - -
116A VAL* 4.3 7.2 - - + -
117A VAL 3.1 6.3 - - - +
118A GLU* 3.9 28.0 - - + -
119A ILE* 4.2 2.0 - - - -
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Residues in contact with TYR 37 (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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36A PHE* 1.3 72.3 - - - +
38A LYS* 1.3 59.8 + - - +
39A THR* 3.7 20.7 - - + +
54A ARG* 4.9 3.1 - - - -
62A PHE* 3.4 30.0 + - - -
63A GLN* 4.7 2.1 - - - +
66A HIS* 3.7 37.8 - + + +
67A LEU 3.4 11.4 - - - -
68A HIS* 5.0 7.0 - - + -
115A LEU* 4.8 9.2 - - + -
116A VAL* 3.4 2.1 - - - -
117A VAL* 2.7 53.2 + - + +
119A ILE* 3.8 17.6 - - + +
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Residues in contact with LYS 38 (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 LEU* 4.7 14.5 - - - +
36A PHE* 3.9 17.9 - - + -
37A TYR* 1.3 79.7 - - - +
39A THR* 1.3 63.2 + - - +
66A HIS* 3.5 0.2 - - - -
67A LEU* 2.8 40.5 + - + +
69A HIS* 3.1 29.5 + - + +
91A SER* 2.7 32.2 + - - +
92A ASP 5.3 0.4 + - - -
95A GLY* 5.0 7.3 - - - -
97A PHE* 3.5 35.2 - - + +
115A LEU 3.2 5.8 - - - -
116A VAL* 4.0 23.3 - - + -
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Residues in contact with THR 39 (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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37A TYR* 3.7 22.4 - - + +
38A LYS* 1.3 75.4 - - - +
40A TRP* 1.3 68.8 + - - +
41A TYR* 4.4 4.5 - - + -
62A PHE* 2.4 49.0 + - + -
65A LEU 3.7 4.4 - - - -
66A HIS* 3.4 14.3 + - - +
97A PHE* 3.3 12.5 - - - -
114A CYS* 3.5 0.9 - - - -
115A LEU* 2.8 47.1 + - + +
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Residues in contact with TRP 40 (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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20A LEU* 3.7 34.5 - - + -
21A THR 4.0 0.7 - - - -
22A CYS* 3.8 10.5 - - - -
39A THR* 1.3 75.0 + - - +
41A TYR* 1.3 66.2 + - - +
57A ILE* 3.9 13.2 - - + -
61A THR 4.5 0.2 - - - -
62A PHE* 3.5 17.2 + - - -
65A LEU* 3.8 16.0 - - + +
89A SER* 3.6 13.7 - - - -
97A PHE* 3.1 59.6 - + - -
98A SER 3.4 8.3 + - - -
99A ILE* 3.6 29.6 - - + -
112A TYR* 4.5 10.8 - + + -
113A CYS 3.2 26.0 - - - -
114A CYS* 3.7 28.9 - - + -
132A MET* 4.1 16.8 - - + -
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Residues in contact with TYR 41 (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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39A THR* 4.4 2.7 - - + -
40A TRP* 1.3 80.0 - - - +
42A ARG* 1.3 72.5 + - - +
43A SER* 4.1 0.9 - - - -
51A CYS* 2.8 34.9 + - - +
53A GLU 3.7 9.6 - - - -
54A ARG* 3.7 45.3 + - + -
55A ARG 3.6 12.8 - - - +
57A ILE* 3.7 13.1 - - - +
62A PHE* 4.0 15.5 - - + +
112A TYR* 3.7 1.0 - - - -
113A CYS* 2.8 47.2 + - + +
115A LEU* 3.7 41.3 - - + +
129A HIS* 4.7 1.4 - - - +
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Residues in contact with ARG 42 (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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41A TYR* 1.3 73.2 - - - +
43A SER* 1.3 63.6 + - - +
53A GLU 3.5 1.2 - - - +
55A ARG* 2.7 50.9 + - + +
56A PRO* 3.0 29.5 + - - +
57A ILE* 3.9 6.8 - - + +
58A ARG* 3.9 15.7 - - - +
107A LEU 2.8 28.9 + - - -
108A ASP* 3.7 5.9 + - - -
109A SER 3.0 20.0 + - - -
110A GLY* 4.2 5.2 - - - -
111A LEU 3.0 12.3 - - - +
112A TYR* 3.5 43.4 + - + -
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Residues in contact with SER 43 (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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41A TYR* 4.1 2.2 - - - -
42A ARG* 1.3 73.4 - - - +
44A SER* 1.3 67.8 + - - -
51A CYS* 3.2 16.6 + - - -
52A SER 3.4 4.7 + - - -
53A GLU* 2.7 29.0 + - - +
55A ARG* 3.2 27.5 + - - +
111A LEU* 2.9 22.4 + - - +
113A CYS* 3.6 25.1 - - - -
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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