Contacts of the strand formed by residues 129 - 134 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94D PHE* 3.2 9.4 - - + +
96D VAL* 4.8 0.9 - - + -
113D LEU* 4.4 12.3 - - + -
116D LEU* 4.1 25.8 - - + -
127D ILE 3.8 2.4 + - - +
128D PRO* 1.3 76.7 - - - +
130D LEU* 1.3 68.5 + - - +
158D CYS* 3.1 32.2 - - + +
159D LEU* 3.3 9.2 + - - +
182D GLU* 5.9 0.2 - - - +
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Residues in contact with LEU 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D ALA* 5.7 0.9 - - + -
94D PHE 2.8 8.3 + - - +
95D LEU* 3.4 18.7 - - + +
96D VAL* 2.7 34.4 + - - +
113D LEU* 5.7 0.2 - - - -
128D PRO 5.5 0.9 - - - -
129D ALA* 1.3 78.9 - - - +
131D LEU* 1.3 58.9 + - - +
132D LEU* 3.9 4.4 + - + -
158D CYS* 4.9 1.1 - - - -
159D LEU* 3.6 32.5 - - + +
161D PHE* 3.7 26.7 - - + -
175D VAL* 3.3 31.2 - - + +
178D GLU* 3.9 5.4 - - + -
179D ALA* 3.9 23.8 - - + -
182D GLU* 4.1 8.7 - - + -
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Residues in contact with LEU 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D VAL* 3.4 18.4 - - + +
98D TYR* 3.7 29.2 - - + -
109D SER* 4.0 17.0 - - - +
113D LEU* 4.2 11.7 - - + -
129D ALA 4.2 0.2 - - - -
130D LEU* 1.3 71.4 - - - +
132D LEU* 1.3 62.2 - - - +
149D GLY 3.5 24.2 - - - +
152D LEU* 3.7 23.8 - - + -
153D ALA* 4.1 6.5 - - - +
158D CYS* 4.2 10.9 - - - -
159D LEU 2.8 15.2 + - - +
160D PHE* 3.3 13.6 - - + -
161D PHE* 2.9 26.7 + - - -
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Residues in contact with LEU 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D LEU* 4.2 19.3 - - + -
95D LEU* 4.0 34.5 - - + -
96D VAL 2.9 13.4 + - - +
97D VAL* 3.4 11.4 - - + -
98D TYR* 3.0 34.1 + - - +
130D LEU* 4.6 9.9 - - + +
131D LEU* 1.3 79.3 - - - +
133D GLY* 1.3 59.1 + - - +
134D ASN 3.3 0.5 + - - -
161D PHE* 3.3 28.9 - - + +
163D VAL* 4.0 16.4 - - + -
175D VAL* 4.0 25.8 - - + -
176D PHE* 5.7 1.1 - - + -
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Residues in contact with GLY 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98D TYR* 3.5 34.5 - - - -
100D VAL* 3.7 9.2 - - - +
132D LEU* 1.3 68.0 - - - +
134D ASN* 1.3 59.4 + - - -
136D LEU 4.6 0.5 + - - -
160D PHE* 4.0 3.3 - - - -
161D PHE 3.0 11.0 + - - -
162D GLU* 3.2 9.9 - - - +
163D VAL* 2.8 31.4 + - - +
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Residues in contact with ASN 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ALA 2.9 24.3 + - - +
32D GLY* 3.5 11.1 + - - -
36D LEU* 3.3 31.6 - - + +
97D VAL* 3.6 10.8 - - + -
98D TYR 2.7 17.8 + - - +
99D SER* 3.3 0.6 - - - -
100D VAL* 2.9 27.2 + - - +
132D LEU 3.3 0.8 + - - -
133D GLY* 1.3 73.1 - - - +
135D LYS* 1.3 78.6 + - - +
136D LEU 3.3 1.3 - - - -
163D VAL* 3.3 6.0 - - + +
164D SER* 3.4 7.4 - - - -
201D GDP 3.3 31.6 + - - +
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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