Contacts of the strand formed by residues 4 - 9 (chain A) in PDB entry 5YL4
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 CYS 4 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG 4.5 0.4 - - - -
3A GLU* 1.3 72.0 - - - +
5A ILE* 1.3 63.6 + - - +
6A SER* 3.9 2.7 + - - -
21A TRP* 6.0 0.7 - - - -
51A THR* 2.8 22.1 + - - +
52A PHE* 3.8 28.1 - - + -
64A ARG* 3.4 14.6 - - - +
133A GLN* 3.5 33.7 - - - -
134A GLY 3.6 4.0 - - - -
136A LEU* 3.8 14.4 - - + -
242A LEU* 4.5 5.8 - - - -
252A LEU* 3.8 24.7 - - - -
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Residues in contact with ILE 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A CYS* 1.3 73.3 - - - +
6A SER* 1.3 71.1 + - - +
7A ILE* 4.3 7.4 - - + -
64A ARG* 3.3 19.5 - - + +
66A VAL* 4.8 4.7 - - + -
122A ILE* 4.3 6.1 - - + +
125A LEU* 3.9 23.6 - - + +
126A ALA* 3.7 30.5 - - + +
129A CYS* 4.5 4.9 - - - -
132A LEU* 3.6 24.5 - - + -
134A GLY 3.0 7.3 + - - -
135A PHE* 3.2 34.8 - - + +
136A LEU* 2.9 23.3 + - - -
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Residues in contact with SER 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A CYS 3.9 2.6 + - - -
5A ILE* 1.3 75.0 - - - +
7A ILE* 1.3 60.9 + - - +
8A HIS* 3.7 24.2 - - - -
21A TRP* 3.9 18.7 + - - -
24A TYR* 5.5 1.0 - - - -
52A PHE* 4.2 13.7 - - - -
64A ARG 2.8 12.4 + - - +
65A ALA* 3.3 2.9 - - - +
66A VAL 3.0 24.4 + - - +
136A LEU* 3.3 21.9 - - - +
138A PHE* 4.1 5.4 - - - -
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Residues in contact with ILE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.3 12.1 - - + +
6A SER* 1.3 76.5 - - - +
8A HIS* 1.3 58.2 + - - +
9A VAL* 3.7 13.2 - - + -
66A VAL* 3.5 11.4 - - + +
68A VAL* 4.6 9.0 - - + -
122A ILE* 3.8 24.0 - - + -
135A PHE* 3.9 20.0 - - + -
136A LEU 2.8 11.9 + - - +
137A VAL* 3.3 10.8 - - + +
138A PHE* 2.7 33.1 + - - +
153A LEU* 3.6 23.8 - - + -
157A LEU* 3.7 30.1 - - + -
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Residues in contact with HIS 8 (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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6A SER* 3.7 13.6 - - - -
7A ILE* 1.3 71.6 - - - +
9A VAL* 1.3 57.4 + - - +
13A GLY 3.4 18.4 - - - +
14A VAL* 3.9 9.2 - - - +
17A GLY* 3.4 26.7 - - - -
20A CYS* 5.7 1.1 - - + -
21A TRP* 3.2 26.7 + + - -
65A ALA* 4.2 1.5 - - + +
66A VAL 2.9 16.1 + - - +
67A PHE* 3.5 29.9 - + + -
68A VAL 2.8 32.4 + - - +
138A PHE* 3.5 41.8 - + - +
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Residues in contact with VAL 9 (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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7A ILE* 3.7 22.9 - - + -
8A HIS* 1.3 74.3 - - - +
10A GLY* 1.3 68.1 + - - +
13A GLY* 3.6 7.6 + - - -
68A VAL* 3.4 11.4 - - + +
137A VAL* 4.5 7.2 - - + -
138A PHE 2.8 21.5 + - - +
139A HIS* 3.6 9.1 - - + +
140A SER* 4.5 0.5 + - - -
145A THR* 3.6 26.2 - - + +
146A GLY* 4.1 2.6 - - - -
149A PHE* 3.9 15.9 - - + -
150A THR* 3.2 28.0 - - - +
153A LEU* 4.2 12.8 - - + -
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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