Contacts of the strand formed by residues 123 - 130 (chain A) in PDB entry 2C10
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 GLU 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A LEU* 4.2 1.0 - - - +
101A LEU* 3.6 14.5 - - - +
102A GLN* 3.0 43.1 + - + +
105A PRO* 5.6 5.9 - - - +
121A ALA* 3.3 18.2 + - - +
122A ARG* 1.3 79.2 - - - +
124A ALA* 1.3 60.1 + - - +
142A VAL* 3.6 17.3 - - + +
143A VAL 3.5 11.4 - - - +
144A GLY* 4.4 0.4 - - - -
146A LEU* 4.2 5.6 - - - +
151A TYR* 2.5 37.9 + - - +
153A ARG* 3.4 15.0 + - - -
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Residues in contact with ALA 124 (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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63A LEU* 3.5 26.7 - - + -
71A VAL* 3.8 26.7 - - + -
99A VAL* 4.1 9.4 - - + -
100A GLU 3.3 5.8 - - - +
102A GLN* 3.8 4.0 - - - +
123A GLU* 1.3 74.7 - - - +
125A LEU* 1.3 60.4 + - - +
126A ALA 4.1 0.2 - - - -
141A LEU 3.7 0.3 - - - +
142A VAL* 3.4 6.1 - - - +
143A VAL* 2.9 32.9 + - + +
146A LEU* 4.4 1.7 - - + +
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Residues in contact with LEU 125 (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 SER* 4.0 1.9 + - - +
99A VAL* 3.6 1.5 - - - -
100A GLU* 2.7 42.8 + - + +
101A LEU 4.8 2.7 - - - +
102A GLN* 3.9 18.6 - - + +
124A ALA* 1.3 74.1 - - - +
126A ALA* 1.3 63.8 + - - +
127A ILE* 4.2 16.8 + - + +
140A GLU* 4.0 28.5 - - + +
141A LEU 3.4 10.5 - - - +
142A VAL* 4.1 10.3 - - + -
155A VAL* 4.2 0.7 - - + -
159A ARG* 3.4 39.7 - - - +
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Residues in contact with ALA 126 (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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71A VAL* 4.9 0.7 - - + -
75A LEU* 3.7 35.7 - - + -
96A VAL* 4.8 0.9 - - + -
98A SER 3.2 11.0 - - - +
99A VAL* 3.8 7.9 - - + -
124A ALA 4.1 0.6 - - - -
125A LEU* 1.3 73.4 - - - +
127A ILE* 1.3 62.2 + - - +
128A VAL* 3.9 6.4 + - + -
139A SER 3.6 1.2 - - - +
140A GLU* 3.6 1.7 - - - -
141A LEU* 2.8 39.4 + - + +
143A VAL* 4.9 5.4 - - + +
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Residues in contact with ILE 127 (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* 3.7 2.9 - - - +
97A PHE* 2.8 33.9 + - + -
98A SER* 2.9 29.6 + - - +
125A LEU* 4.2 14.3 - - + +
126A ALA* 1.3 73.9 - - - +
128A VAL* 1.3 62.2 + - - +
129A PHE* 3.8 26.2 - - + -
138A VAL* 3.9 15.7 - - + -
139A SER 3.5 2.9 - - - -
140A GLU* 4.3 19.1 - - + +
344A PHE* 3.8 23.3 - - + -
647A VAL* 4.4 7.4 - - + -
648A PHE* 4.3 16.4 - - + -
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Residues in contact with VAL 128 (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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75A LEU* 5.1 1.1 - - + -
79A LEU* 4.1 18.2 - - + -
83A LEU* 4.7 2.5 - - + -
95A CYS 3.3 18.4 - - - +
96A VAL* 4.5 8.7 - - + -
126A ALA* 4.4 8.5 - - + +
127A ILE* 1.3 77.0 - - - +
129A PHE* 1.3 71.5 + - - +
130A PHE* 3.7 37.4 + - + -
138A VAL* 3.3 5.7 - - - +
139A SER 2.9 32.6 + - - +
141A LEU* 3.6 28.9 - - + -
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Residues in contact with PHE 129 (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 ASP 3.3 0.9 - - - +
94A ASN* 3.2 7.3 - - - +
95A CYS* 2.8 48.5 + - - +
97A PHE* 3.5 35.4 - + + -
127A ILE* 3.8 12.1 - - + -
128A VAL* 1.3 79.0 - - - +
130A PHE* 1.3 61.6 + - - +
131A GLY 3.3 2.8 + - - -
137A ASN 4.1 2.5 - - - -
138A VAL* 4.1 10.8 - - + -
166A TYR* 3.8 13.2 - - + +
169A ARG* 3.2 47.8 - - + -
170A PRO* 3.9 13.0 - - + -
172A LEU* 3.7 32.5 - - + -
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Residues in contact with PHE 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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79A LEU* 3.8 31.0 - - + -
83A LEU* 6.1 0.4 - - + -
94A ASN* 3.1 31.6 - - + -
128A VAL* 3.7 34.5 - - + -
129A PHE* 1.3 70.3 - - - +
131A GLY* 1.3 56.7 + - - +
132A ARG 3.4 0.4 - - - -
133A GLN* 3.5 22.3 - - - +
136A PRO* 3.3 6.9 - - - +
137A ASN* 2.8 38.5 + - - +
139A SER* 3.7 30.7 - - - -
141A LEU* 4.7 6.1 - - + -
166A TYR* 3.9 1.8 - - - -
1E NAG 3.7 29.2 - - - +
2E NAG 4.8 7.2 - - - -
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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