Contacts of the strand formed by residues 15 - 24 (chain X) in PDB entry 2BIT
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 15 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11X ASP* 3.5 4.5 + - - -
12X ALA* 2.9 30.3 + - - +
13X ASN 4.1 7.4 - - - +
14X GLY* 1.3 86.8 + - - +
16X PRO* 1.3 77.4 - - + +
17X LEU* 4.5 2.3 - - - +
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Residues in contact with PRO 16 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL 3.7 2.2 - - - +
11X ASP* 3.3 17.2 - - - +
14X GLY 4.5 1.6 - - - +
15X LYS* 1.3 94.9 - - + +
17X LEU* 1.3 63.4 - - - +
18X GLY* 4.4 6.3 - - - +
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Residues in contact with LEU 17 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10X VAL* 2.7 25.0 + - + +
12X ALA* 4.0 32.3 - - + +
15X LYS 3.5 1.3 + - - +
16X PRO* 1.3 77.0 - - - +
18X GLY* 1.3 57.6 + - - +
137X ASP* 5.0 2.9 - - - +
138X VAL* 3.5 24.3 - - + +
141X LYS* 4.1 40.4 - - + +
142X ILE* 4.0 28.5 - - + +
145X PHE* 4.4 4.9 - - + -
156X ILE* 5.1 0.9 - - + -
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Residues in contact with GLY 18 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8X LEU 3.9 0.2 - - - +
9X ASP* 3.5 5.6 - - - +
10X VAL* 3.0 26.2 + - - +
16X PRO* 3.5 7.4 - - - +
17X LEU* 1.3 80.9 - - - +
19X ARG* 1.3 60.1 + - - -
138X VAL* 3.8 9.3 - - - +
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Residues in contact with ARG 19 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X TYR* 3.4 41.4 + - + -
8X LEU 3.4 4.3 - - - +
9X ASP* 2.8 38.5 + - - +
18X GLY* 1.3 73.6 - - - -
20X VAL* 1.3 67.0 + - - +
21X VAL* 3.9 16.4 - - + -
134X GLU* 3.9 12.5 - - - +
135X GLY* 3.4 20.4 + - - -
138X VAL* 3.7 5.8 - - - +
164X LEU* 3.9 25.3 - - - +
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Residues in contact with VAL 20 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7X TYR* 3.2 4.7 - - - +
8X LEU* 2.8 49.4 + - + +
10X VAL* 4.6 8.3 - - + -
19X ARG* 1.3 72.1 - - - +
21X VAL* 1.3 62.2 + - - +
22X LEU* 3.9 27.3 + - + +
53X PHE* 6.1 0.9 - - + -
114X ILE* 4.2 9.2 - - + -
132X VAL* 4.2 6.1 - - + -
134X GLU 3.6 8.7 - - - +
135X GLY 4.0 1.3 - - - +
138X VAL* 3.7 31.0 - - + -
139X VAL* 4.0 26.7 - - + -
142X ILE* 5.0 3.1 - - + -
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Residues in contact with VAL 21 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5X LEU* 4.6 11.7 - - + -
6X VAL 3.3 10.1 - - - +
19X ARG* 3.9 24.2 - - + -
20X VAL* 1.3 76.7 - - - +
22X LEU* 1.3 64.5 + - - +
132X VAL* 3.5 5.0 - - - +
133X ILE* 2.8 45.0 + - + -
134X GLU* 2.9 44.2 + - + +
164X LEU* 3.8 24.2 - - + -
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Residues in contact with LEU 22 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4X PRO 3.8 0.2 - - - +
5X LEU* 3.3 5.2 - - - +
6X VAL* 2.8 47.4 + - + +
8X LEU* 4.0 24.2 - - + -
20X VAL* 3.9 13.0 - - + +
21X VAL* 1.3 76.2 - - - +
23X GLU* 1.3 60.1 + - - +
24X LEU* 4.4 0.9 - - + -
36X PHE* 3.7 33.4 - - + -
98X LEU* 3.9 27.4 - - + -
114X ILE* 4.3 8.1 - - + -
131X HIS 3.4 11.0 - - - +
132X VAL* 3.8 29.6 - - + -
133X ILE* 4.2 3.4 - - - -
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Residues in contact with GLU 23 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ASN* 3.0 36.0 - - + +
4X PRO 3.5 5.8 - - - +
5X LEU* 3.8 9.9 - - + -
22X LEU* 1.3 72.4 - - - +
24X LEU* 1.3 66.7 + - - +
25X LYS* 3.2 25.0 + - - +
130X GLY* 3.0 25.5 - - - -
131X HIS* 3.0 31.2 + - + -
133X ILE* 3.6 26.2 - - + +
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Residues in contact with LEU 24 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3X ASN* 3.1 20.8 - - - +
4X PRO* 2.9 23.5 + - + +
6X VAL* 3.9 24.2 - - + -
22X LEU* 4.4 0.9 - - + -
23X GLU* 1.3 75.4 - - - +
25X LYS* 1.3 59.3 + - - +
26X ALA 2.8 11.0 + - - -
33X ALA* 3.5 35.4 - - + +
36X PHE* 3.6 26.7 - - + -
37X ARG* 3.7 24.7 - - + +
98X LEU* 3.7 22.4 - - + -
129X PHE* 3.5 10.3 - - + +
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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