Contacts of the strand formed by residues 129 - 134 (chain A) in PDB entry 3C5C
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 129 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A PHE* 3.3 8.7 - - + +
96A VAL* 4.9 2.0 - - + -
113A LEU* 4.5 8.7 - - + -
116A LEU* 3.8 29.8 - - + -
127A ILE 3.6 2.4 + - - +
128A PRO* 1.3 75.9 - - - +
130A LEU* 1.3 68.6 + - - +
158A CYS* 3.2 33.3 - - + +
159A LEU* 3.2 10.0 + - - +
182A GLU* 5.3 1.8 + - - +
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Residues in contact with LEU 130 (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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93A ALA* 5.3 0.9 - - + -
94A PHE 2.7 14.9 + - - +
95A LEU* 3.3 15.9 - - + +
96A VAL* 2.8 32.0 + - - -
128A PRO 5.0 1.8 - - - +
129A ALA* 1.3 83.4 - - - +
131A LEU* 1.3 56.6 + - - +
132A LEU* 3.8 7.6 + - + +
159A LEU* 3.8 11.9 - - + -
161A PHE* 3.7 29.8 - - + -
175A VAL* 3.3 29.2 - - + +
178A GLU* 4.3 4.9 - - + -
179A ALA* 3.8 29.8 - - + +
182A GLU* 4.3 17.0 - - + -
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Residues in contact with LEU 131 (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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96A VAL* 3.4 19.3 - - + +
98A TYR* 3.8 27.1 - - + -
109A SER* 4.0 15.3 - - - +
113A LEU* 4.3 12.3 - - + -
129A ALA 4.1 0.8 - - - -
130A LEU* 1.3 71.5 - - - +
132A LEU* 1.3 62.2 + - - +
133A GLY 4.2 0.2 - - - -
149A GLY* 3.4 25.6 - - - +
152A LEU* 3.9 16.8 - - + -
153A ALA* 3.7 15.7 - - + +
158A CYS* 3.8 12.2 - - - -
159A LEU 2.8 16.9 + - - +
160A PHE* 3.3 10.4 - - + -
161A PHE* 3.0 26.2 + - - +
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Residues in contact with LEU 132 (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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36A LEU* 4.3 19.1 - - + -
95A LEU* 4.1 31.9 - - + -
96A VAL 2.7 13.5 + - - +
97A VAL* 3.4 9.9 - - + -
98A TYR* 2.8 34.2 + - - +
130A LEU* 4.4 13.2 - - + +
131A LEU* 1.3 83.6 - - - +
133A GLY* 1.3 59.9 + - - +
134A ASN 3.5 0.4 + - - -
161A PHE* 3.3 34.8 - - + +
163A VAL* 4.3 14.1 - - + -
175A VAL* 4.2 23.6 - - + -
176A PHE* 5.7 0.7 - - + -
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Residues in contact with GLY 133 (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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98A TYR* 3.4 34.7 - - - -
100A VAL* 3.6 9.2 - - - +
132A LEU* 1.3 68.8 - - - +
134A ASN* 1.3 62.5 + - - -
136A LEU 4.8 0.2 + - - -
160A PHE* 4.2 1.2 - - - -
161A PHE 2.9 13.2 + - - -
162A GLU* 3.1 11.6 - - - +
163A VAL* 2.9 25.5 + - - +
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Residues in contact with ASN 134 (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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31A ALA 2.9 23.3 + - - +
32A GLY* 3.5 10.9 + - - -
36A LEU* 3.5 19.3 - - + +
97A VAL* 3.8 11.7 - - + -
98A TYR 2.6 17.0 + - - +
99A SER* 3.5 0.3 - - - -
100A VAL* 2.9 25.8 + - - +
132A LEU 3.5 0.2 + - - -
133A GLY* 1.3 74.2 - - - +
135A LYS* 1.3 82.0 + - - +
136A LEU 3.4 0.4 - - - -
163A VAL* 3.2 9.0 - - + +
164A SER* 3.3 20.1 - - - -
165A ALA 3.4 4.0 + - - -
201A GDP 3.3 26.3 + - - +
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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