Contacts of the strand formed by residues 143 - 148 (chain P) in PDB entry 5C7O
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 HIS 143 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95P MET* 4.8 15.7 - - + -
99P VAL 5.6 0.2 - - - -
100P LYS* 3.7 34.2 + - + +
101P VAL* 2.4 42.1 + - + -
102P VAL* 5.0 3.8 - - + -
138P LEU 3.6 1.4 - - - +
139P VAL* 3.3 4.4 - - - -
140P VAL 2.8 35.1 + - - +
141P ASP 3.1 3.9 + - - +
142P ASN* 1.3 75.9 - - - +
144P GLU* 1.3 79.2 + - - +
145P ILE* 3.6 18.0 + - + +
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Residues in contact with GLU 144 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101P VAL 4.3 0.9 - - - +
102P VAL* 4.6 3.6 - - - +
134P ARG* 4.8 12.9 + - - +
135P ASN* 5.5 3.8 + - - -
137P GLN* 3.4 32.0 + - - +
138P LEU 3.8 3.4 - - - -
139P VAL* 4.3 15.9 - - + -
142P ASN 3.5 8.0 + - - +
143P HIS* 1.3 93.8 + - - +
145P ILE* 1.3 60.6 + - - +
146P SER 4.2 0.6 + - - -
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Residues in contact with ILE 145 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91P LEU* 4.1 32.1 - - + -
95P MET* 5.5 0.4 - - - -
101P VAL* 3.7 16.8 - - + +
102P VAL 3.8 2.5 - - - -
103P ALA* 3.7 19.5 - - - +
104P VAL* 3.8 17.3 - - + -
137P GLN* 3.4 7.9 - - - +
138P LEU* 2.7 49.3 + - + +
140P VAL* 4.2 22.7 - - + -
143P HIS* 3.7 15.9 - - + +
144P GLU* 1.3 77.0 - - - +
146P SER* 1.3 73.9 + - - +
147P VAL* 3.8 0.6 - - + +
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Residues in contact with SER 146 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102P VAL 3.0 18.7 + - - -
103P ALA* 3.1 4.5 - - - +
104P VAL 2.8 26.5 + - - +
137P GLN* 3.6 22.0 + - - +
144P GLU 4.3 0.2 + - - -
145P ILE* 1.3 75.0 - - - +
147P VAL* 1.3 60.1 + - - +
148P TYR* 3.9 27.7 + - - -
161P VAL* 3.9 9.5 - - - +
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Residues in contact with VAL 147 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104P VAL* 3.3 4.0 - - + +
111P PRO* 3.9 23.0 - - + +
114P MET* 3.6 35.0 - - + -
136P GLY 3.8 20.1 + - - +
138P LEU* 3.6 29.8 - - + +
145P ILE* 3.6 1.3 + - + +
146P SER* 1.3 78.3 - - - +
148P TYR* 1.3 70.2 + - - +
149P GLN* 3.6 27.9 - - - +
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Residues in contact with TYR 148 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P ALA* 3.7 25.1 - - + -
104P VAL 2.8 9.1 + - - +
105P ASN* 3.1 19.6 - - + +
106P ASP 3.1 17.7 + - - -
146P SER* 3.9 17.9 + - - -
147P VAL* 1.3 77.2 - - - +
149P GLN* 1.3 75.5 + - - +
150P CYS* 4.7 1.8 - - - +
156P ILE* 3.7 18.4 - - + -
157P PRO* 3.6 43.2 + - + -
158P TRP* 4.5 6.7 - + - -
160P ALA* 3.5 18.3 - - + +
161P VAL* 3.3 24.1 - - + +
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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