Contacts of the strand formed by residues 6 - 18 (chain B) in PDB entry 5XOU
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 LYS 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B GLY* 1.3 75.8 - - - -
7B THR* 1.3 71.1 + - - +
8B GLU* 5.4 2.9 - - - -
312B GLN* 3.4 43.1 - - + +
313B ALA 3.7 4.7 - - - -
314B TYR* 4.1 18.5 - - + +
315B ARG* 5.1 2.8 + - - -
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Residues in contact with THR 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 LYS* 1.3 83.8 - - - +
8B GLU* 1.3 78.0 + - - +
9B VAL* 5.2 1.5 - - + +
312B GLN* 3.6 8.1 - - - +
313B ALA* 2.8 49.2 + - + +
315B ARG* 4.0 35.1 + - + +
592B LEU* 4.2 6.5 - - + -
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Residues in contact with GLU 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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6B LYS* 5.4 2.5 - - - -
7B THR* 1.3 90.7 + - - +
9B VAL* 1.3 68.8 + - - +
310B ARG* 2.8 45.3 + - + +
311B ALA 3.5 11.4 - - - +
312B GLN* 4.0 20.3 + - - +
583B PRO* 4.3 1.4 - - - +
584B VAL* 3.4 27.2 + - + +
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Residues in contact with VAL 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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7B THR* 5.2 1.8 - - + +
8B GLU* 1.3 81.4 - - - +
10B PHE* 1.3 66.9 + - - +
11B LEU* 4.2 13.0 - - + -
310B ARG* 3.1 6.8 - - - +
311B ALA* 2.9 43.1 + - + +
313B ALA* 3.7 24.5 - - + -
581B VAL* 4.6 5.8 - - + -
582B TYR 3.3 16.8 - - - +
583B PRO* 4.6 5.6 - - + -
584B VAL* 3.9 7.6 - - - -
592B LEU* 4.2 21.3 - - + -
594B VAL* 4.2 15.0 - - + -
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Residues in contact with PHE 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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9B VAL* 1.3 75.1 - - - +
11B LEU* 1.3 70.2 + - - +
287B ARG* 4.8 9.2 - - - -
291B ARG* 3.7 29.2 - - - +
308B ALA* 3.9 26.0 - - + -
309B VAL 3.2 8.1 - - - +
310B ARG* 3.6 52.3 - - + -
581B VAL* 3.4 4.9 - - - -
582B TYR* 2.8 43.8 + - + +
583B PRO 4.1 7.6 - - - -
584B VAL* 3.7 33.0 - - + -
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Residues in contact with LEU 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 VAL* 4.2 11.2 - - + -
10B PHE* 1.3 84.9 - - - +
12B ASN* 1.3 60.3 + - - +
13B ARG* 2.8 57.4 + - + +
14B PHE* 5.0 2.4 - - - -
308B ALA* 5.0 2.9 - - - +
309B VAL* 2.9 27.6 + - + +
311B ALA* 4.4 15.5 - - + -
580B ARG 3.4 6.5 - - - +
581B VAL* 3.7 27.1 - - + -
582B TYR* 5.0 2.6 - - - -
594B VAL* 4.7 3.1 - - + -
596B LEU* 4.1 18.8 - - + -
602B LEU* 4.3 10.3 - - + -
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Residues in contact with ASN 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 LEU* 1.3 69.5 - - - +
13B ARG* 1.3 59.9 + - - +
14B PHE* 4.1 10.3 - - - -
165B LEU 3.7 0.5 - - - +
166B GLU* 3.3 24.6 + - - +
167B VAL* 3.0 47.3 + - - +
168B ASP* 3.8 16.1 + - - +
290B THR* 4.3 7.2 - - + -
579B GLY* 3.7 4.9 - - - -
580B ARG* 2.8 46.3 + - + +
582B TYR* 4.2 14.5 - - + +
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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 LEU* 2.8 37.8 + - + +
12B ASN* 1.3 85.1 + - - +
14B PHE* 1.3 67.5 + - - +
156B TRP* 3.5 39.0 - - + +
164B LEU* 5.1 6.5 - - + +
165B LEU 3.1 9.0 - - - +
166B GLU* 4.1 15.2 + - + -
308B ALA* 3.7 0.7 - - - -
309B VAL* 3.1 40.4 + - + +
578B GLY 4.7 12.7 + - - -
579B GLY* 5.6 0.6 - - - -
596B LEU* 4.2 23.2 - - - +
602B LEU* 5.4 0.6 - - - +
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Residues in contact with PHE 14 (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 LEU 5.1 0.9 - - - -
12B ASN* 4.1 11.7 - - - -
13B ARG* 1.3 79.3 - - - +
15B ALA* 1.3 64.4 + - - +
16B LEU* 3.4 2.1 + - + +
164B LEU* 3.6 4.2 - - - -
165B LEU* 2.8 51.5 + - + +
167B VAL* 4.4 7.2 - - + -
290B THR* 3.7 31.2 - - + -
291B ARG* 4.3 18.6 - - + -
294B ALA* 3.5 33.0 - - + -
306B PRO* 3.9 23.1 - - + -
307B GLU 3.6 4.3 - - - +
308B ALA* 3.5 37.9 - - + -
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Residues in contact with ALA 15 (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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14B PHE* 1.3 70.4 - - - +
16B LEU* 1.3 64.5 + - - +
162B ALA* 5.8 2.7 - - + -
163B PHE 3.6 5.2 - - - +
164B LEU* 3.8 15.4 - - + +
305B THR 3.8 2.8 - - - +
306B PRO* 3.5 4.3 - - - +
307B GLU* 2.9 44.3 + - + +
309B VAL* 4.2 6.0 - - + +
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Residues in contact with LEU 16 (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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14B PHE 4.0 5.6 - - - +
15B ALA* 1.3 77.4 - - - +
17B ARG* 1.3 69.5 + - - +
18B PRO* 4.2 1.2 - - - +
155B LEU* 4.3 7.4 - - + -
162B ALA* 3.6 12.3 - - - +
163B PHE* 2.6 21.7 + - + +
165B LEU* 4.0 30.3 - - + +
297B ILE* 5.9 0.4 - - + -
298B GLY* 4.6 6.7 - - - -
303B LEU* 3.3 42.8 - - + +
304B GLY 4.1 5.4 - - - +
305B THR 4.0 5.4 - - - -
306B PRO* 3.4 41.3 - - + -
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Residues in contact with ARG 17 (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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16B LEU* 1.3 77.1 - - - +
18B PRO* 1.3 88.1 + - + +
20B ASN* 3.6 15.5 - - - +
23B GLU* 2.6 42.2 + - - -
116B LEU* 5.3 0.4 - - - +
120B ARG* 4.9 10.5 - - - +
162B ALA* 3.8 0.4 - - - -
163B PHE* 2.7 52.2 + - + -
302B GLY 3.7 18.7 + - - -
303B LEU* 2.9 29.7 + - - +
304B GLY* 4.8 4.2 - - - +
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Residues in contact with PRO 18 (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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16B LEU 4.2 2.7 - - - +
17B ARG* 1.3 108.9 + - + +
19B LEU* 1.3 66.5 + - - +
20B ASN* 3.4 1.0 + - - +
160B SER 5.5 2.2 - - - +
161B GLY 3.2 12.1 - - - +
162B ALA* 3.5 9.2 - - + -
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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