Contacts of the strand formed by residues 120 - 127 (chain A) in PDB entry 2Q7N
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 SER 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A MET* 4.4 3.6 - - - +
117A PRO 3.6 8.6 + - - -
118A HIS 2.9 4.1 + - - -
119A PRO* 1.3 73.3 + - - +
121A ASN* 1.3 61.9 + - - +
122A ALA* 3.5 2.2 + - - +
144A THR* 4.6 2.5 + - - -
145A MET* 3.2 57.2 + - - +
176A ILE* 5.3 2.0 - - - -
177A ASP 2.9 22.1 + - - -
178A SER* 3.3 21.8 + - - -
179A PRO* 4.7 2.0 - - - -
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Residues in contact with ASN 121 (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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119A PRO 4.3 0.4 - - - -
120A SER* 1.3 68.0 - - - +
122A ALA* 1.3 65.8 + - - +
123A THR* 4.1 1.7 + - - +
142A LEU 3.5 15.3 - - - +
143A ASN 4.1 0.2 - - - +
144A THR* 4.3 15.6 + - - +
175A HIS* 4.6 0.3 - - - +
177A ASP* 3.1 40.9 + - + +
179A PRO* 5.6 1.4 - - - +
1E NAG 1.4 78.3 + - + +
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Residues in contact with ALA 122 (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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116A LEU* 6.2 0.7 - - + -
120A SER* 3.5 8.1 + - - +
121A ASN* 1.3 76.6 + - - +
123A THR* 1.3 63.9 + - - +
124A TRP* 3.8 14.1 + - - +
142A LEU 3.4 4.3 - - - +
143A ASN* 2.5 30.0 + - - +
145A MET* 5.1 7.9 - - + -
174A TRP* 5.2 7.6 - - + -
175A HIS 3.3 13.5 - - - +
176A ILE* 3.8 23.8 - - + -
177A ASP 4.4 0.2 - - - +
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Residues in contact with THR 123 (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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121A ASN* 4.1 7.1 + - - +
122A ALA* 1.3 72.8 - - - +
124A TRP* 1.3 62.7 + - - +
140A VAL* 5.9 4.9 - - + -
141A LEU 3.4 10.3 - - - +
142A LEU* 3.2 29.4 - - - +
174A TRP* 3.6 0.5 - - - -
175A HIS* 2.8 55.3 + - - +
187A TRP* 3.8 9.3 - - - -
1E NAG 4.6 17.2 + - - +
2E NAG 5.1 5.2 - - + -
3E FUC 4.2 13.4 + - - +
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Residues in contact with TRP 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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91A PRO* 4.6 8.3 - - + -
109A TRP* 3.3 61.9 - + + -
110A ASN 4.5 2.9 - - - -
111A ASP* 4.2 11.9 - - + -
122A ALA* 3.8 9.6 + - - +
123A THR* 1.3 85.1 - - - +
125A GLU* 1.3 59.7 + - - +
126A ILE* 3.6 5.0 + - + +
140A VAL* 3.1 10.2 - - - +
141A LEU* 3.0 41.7 + - + +
143A ASN* 3.6 30.0 - - + +
172A ILE* 3.6 28.7 - - + -
173A ARG 3.5 5.8 - - - -
174A TRP* 3.2 48.8 - + + +
187A TRP* 4.6 0.9 - - - -
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Residues in contact with GLU 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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124A TRP* 1.3 71.3 - - - +
126A ILE* 1.3 65.0 + - - +
138A ALA* 4.1 16.9 - - + +
140A VAL* 3.7 24.5 - - + +
172A ILE* 3.6 2.7 - - - -
173A ARG* 2.8 59.9 + - + -
187A TRP* 4.0 10.3 - - + -
190A TRP* 3.0 38.2 - - + -
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Residues in contact with ILE 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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107A LEU* 3.7 20.6 - - + -
109A TRP* 4.3 8.7 - - + +
124A TRP* 3.6 3.3 + - + +
125A GLU* 1.3 79.9 - - - +
127A LYS* 1.3 75.6 + - - +
138A ALA* 3.4 3.1 - - - -
139A LEU 3.2 35.1 + - - +
141A LEU* 3.7 17.9 - - + -
155A TRP* 3.4 65.1 - - + -
170A VAL* 4.4 5.8 - - + -
171A SER 3.3 9.6 - - - +
172A ILE* 3.5 18.2 - - + -
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Residues in contact with LYS 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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126A ILE* 1.3 79.9 - - - +
128A VAL* 1.3 75.7 + - - +
129A LEU* 4.8 8.9 - - + +
135A GLU* 4.3 10.1 - - + -
137A VAL 3.5 6.5 - - - +
138A ALA* 3.7 18.4 - - + +
170A VAL* 3.3 1.3 - - - -
171A SER* 2.6 62.3 + - - +
190A TRP* 3.8 44.7 - - + +
193A LEU* 4.8 14.8 - - - +
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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