Contacts of the strand formed by residues 5 - 13 (chain B) in PDB entry 3U53
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 ALA 5 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B ARG* 1.3 74.7 - - - +
6B CYS* 1.3 66.0 + - - +
42B LYS* 4.5 2.9 - - + -
43B GLY* 3.0 27.6 - - - +
44B HIS* 4.1 2.0 - - + +
45B VAL 4.3 0.9 - - - +
89B LYS* 3.7 26.9 - - - +
90B THR 3.0 9.4 + - - +
91B VAL* 3.2 14.3 - - + -
92B ILE* 2.9 23.7 + - - +
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Residues in contact with CYS 6 (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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4B ARG* 4.8 0.7 - - - -
5B ALA* 1.3 81.0 - - - +
7B GLY* 1.3 59.4 + - - +
42B LYS* 3.2 5.8 - - - -
43B GLY 2.8 30.4 + - - +
45B VAL* 3.9 11.7 - - - -
51B ASP* 3.4 54.5 - - - +
54B THR* 3.8 9.8 - - - +
55B ALA* 3.8 11.4 - - + +
58B GLU* 4.1 3.3 - - - +
91B VAL* 4.8 0.7 - - - -
92B ILE* 3.3 20.2 - - + +
94B TRP* 4.7 0.7 - - + -
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Residues in contact with GLY 7 (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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6B CYS* 1.3 76.0 - - - +
8B LEU* 1.3 68.3 + - - +
41B PRO 3.1 15.7 - - - -
42B LYS* 3.5 6.0 - - - +
55B ALA* 3.3 19.0 - - - +
91B VAL* 4.8 0.2 - - - +
92B ILE 2.8 9.9 + - - -
93B TYR* 3.5 10.5 - - - -
94B TRP* 3.4 12.8 + - - -
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Residues in contact with LEU 8 (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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7B GLY* 1.3 82.4 - - - +
9B ILE* 1.3 60.6 + - - +
10B ILE* 3.0 18.7 + - + -
40B PRO* 3.4 14.0 - - - +
41B PRO* 3.1 16.9 + - - +
55B ALA* 3.8 16.4 - - + +
56B LEU* 4.1 12.8 - - + -
59B THR* 3.3 28.2 + - - +
70B LEU* 4.0 15.5 - - + -
72B ILE* 3.9 13.5 - - + -
93B TYR* 3.6 5.5 - - - -
94B TRP* 3.5 32.8 - - + +
96B ALA* 4.0 19.7 - - + -
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Residues in contact with ILE 9 (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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8B LEU* 1.3 70.2 - - - +
10B ILE* 1.3 58.0 + - - +
11B PHE 3.7 0.2 + - - -
26B PHE* 3.7 29.6 - - + -
40B PRO* 4.2 15.7 - - + -
76B PHE* 4.4 16.2 - - + -
78B ARG* 5.6 0.2 - - + -
93B TYR* 3.9 31.6 - - + -
94B TRP 2.9 12.1 + - - +
95B LEU* 3.7 17.8 - - + +
96B ALA 3.1 21.1 + - - +
131B MET* 5.7 0.9 - - + -
134B ALA* 4.1 31.9 - - + +
135B LEU* 3.9 16.8 - - + -
138B GLY* 5.4 1.1 - - - -
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Residues in contact with ILE 10 (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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8B LEU* 3.0 18.2 + - + +
9B ILE* 1.3 72.7 - - - +
11B PHE* 1.3 64.7 + - - +
26B PHE* 3.3 8.7 - - - +
27B LEU* 3.0 40.9 + - + +
40B PRO* 4.9 2.4 - - - +
41B PRO* 4.2 14.1 - - + -
59B THR* 4.0 18.8 - - + -
65B ILE* 4.5 4.9 - - + -
70B LEU* 3.4 30.7 - - + -
96B ALA* 3.5 13.5 - - + +
98B VAL* 3.7 25.1 - - + -
116B TRP* 3.9 13.2 - - + -
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Residues in contact with PHE 11 (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 ILE 4.2 0.2 - - - -
10B ILE* 1.3 76.5 - - - +
12B ARG* 1.3 71.5 + - - +
13B ARG* 4.1 15.9 - - + -
24B ILE* 4.0 15.7 - - + -
25B GLU 3.0 13.5 - - - +
26B PHE* 3.7 17.5 - - + -
73B ILE* 3.9 15.9 - - + -
95B LEU* 3.7 20.2 - - + -
96B ALA 2.9 35.1 + - - -
97B GLU* 3.3 35.1 - - + -
98B VAL* 3.0 26.8 + - - +
116B TRP* 3.9 4.9 - - - -
142B LEU* 3.8 29.4 - - + -
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Residues in contact with ARG 12 (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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11B PHE* 1.3 75.7 - - - +
13B ARG* 1.3 65.0 + - - +
14B CYS* 4.0 2.0 + - - -
23B ALA 3.5 0.2 - - - +
24B ILE* 3.3 4.3 - - - -
25B GLU* 2.6 64.7 + - + +
97B GLU* 5.0 1.3 - - - -
98B VAL* 3.2 24.2 - - + +
101B TYR* 2.8 71.9 + - + +
116B TRP* 3.2 57.9 - - + +
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Residues in contact with ARG 13 (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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11B PHE* 4.1 19.2 - - + -
12B ARG* 1.3 77.6 - - - +
14B CYS* 1.3 63.5 + - - +
15B LEU* 3.8 34.5 + - + +
23B ALA* 2.9 11.1 - - + +
24B ILE* 3.8 16.7 - - + +
73B ILE* 5.8 2.2 - - - +
97B GLU* 2.7 37.5 + - - +
98B VAL 5.6 0.6 + - - -
101B TYR* 4.1 12.5 - - - +
142B LEU* 4.6 14.5 + - - +
146B GLU* 5.8 7.7 - - - +
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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