Contacts of the strand formed by residues 9 - 14 (chain A) in PDB entry 1U5H
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 GLY 9 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A GLY 3.3 0.4 - - - -
8A PRO* 1.3 79.7 - - - +
10A TRP* 1.3 61.1 + - - -
28A ALA* 3.8 4.0 - - - +
29A ASP* 2.8 44.1 + - - +
30A VAL 3.4 0.2 + - - -
206A THR 4.2 0.9 - - - -
214A ILE* 3.9 19.7 - - - -
217A VAL* 4.0 13.2 - - - -
218A ARG* 4.8 1.1 - - - +
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Residues in contact with TRP 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 4.0 21.5 + - + -
6A ALA* 5.1 0.6 - - - +
7A GLY 3.3 22.5 + - - -
8A PRO 3.4 2.8 + - - -
9A GLY* 1.3 78.4 - - - -
11A LEU* 1.3 56.1 + - - +
30A VAL* 3.2 49.1 - - + +
32A ILE* 4.0 21.1 - - + -
62A VAL* 4.1 8.3 - - + -
89A MET* 5.0 0.4 - - + -
108A ILE* 3.4 34.3 - - + -
176A LEU* 3.7 25.8 - - + -
178A LEU* 3.8 16.2 - - + -
205A VAL* 3.3 30.0 - - + +
206A THR 3.6 2.6 + - - -
207A VAL* 4.5 4.5 - - + -
208A CYS* 2.7 37.2 + - - +
214A ILE* 4.1 0.7 - - - -
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Residues in contact with LEU 11 (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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10A TRP* 1.3 76.3 - - - +
12A PHE* 1.3 76.0 + - - +
13A CYS 3.6 0.3 + - - -
24A ALA* 4.0 36.3 - - + +
27A ALA* 4.7 2.7 - - + -
28A ALA* 3.6 18.6 - - + -
30A VAL 2.9 7.9 + - - -
31A VAL* 3.4 6.9 - - - +
32A ILE* 2.9 26.2 + - - +
208A CYS* 3.4 9.2 - - + +
209A ILE 3.8 1.1 - - - -
210A HIS* 3.6 39.0 - - - +
211A PRO* 3.9 23.6 - - + -
214A ILE* 4.0 4.3 - - + -
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Residues in contact with PHE 12 (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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11A LEU* 1.3 88.5 - - - +
13A CYS* 1.3 60.0 + - - +
14A PRO* 4.3 4.5 - - + +
32A ILE* 3.4 34.7 - - + +
34A ASP* 4.2 11.4 - - + +
64A ARG* 3.4 49.1 - - - -
89A MET* 4.0 13.7 - - - -
133A MET* 4.1 8.7 - - + -
181A VAL* 3.9 12.6 - - + -
207A VAL* 3.4 29.4 - - + -
208A CYS 3.0 17.1 + - - +
209A ILE* 4.0 24.8 - - + +
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Residues in contact with CYS 13 (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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11A LEU 3.6 0.2 + - - -
12A PHE* 1.3 75.1 - - - +
14A PRO* 1.3 78.6 - - - +
15A ALA 3.3 0.2 + - - -
17A ALA* 5.4 0.2 - - - -
20A ALA* 4.2 19.3 - - - -
21A PHE* 3.8 28.0 - - - -
24A ALA* 4.1 20.2 - - + -
31A VAL* 3.9 21.8 - - + -
32A ILE 2.9 8.3 + - - -
33A LEU* 3.4 7.7 - - + +
34A ASP* 2.9 22.1 + - - -
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Residues in contact with PRO 14 (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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12A PHE* 4.4 5.2 - - + +
13A CYS* 1.3 89.0 - - + +
15A ALA* 1.3 60.0 + - - +
16A ASP* 3.2 22.1 + - - +
17A ALA* 3.4 19.4 + - + +
21A PHE* 3.4 8.8 - - - -
34A ASP* 3.9 12.3 - - + +
38A GLY* 3.5 29.4 - - - +
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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