Contacts of the strand formed by residues 122 - 127 (chain A) in PDB entry 2GRU
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A PHE* 3.3 40.6 - - + -
94A ARG 5.5 1.0 + - - -
96A THR 4.0 2.4 + - - +
97A ALA* 3.5 9.1 - - + -
98A ILE* 2.8 34.8 + - - +
114A ALA* 4.3 0.9 - - - +
121A ILE* 1.3 77.1 - - - +
123A LEU* 1.3 57.8 + - - +
124A ILE* 5.2 0.4 - - + -
157A TYR* 4.9 0.2 - - - -
160A ARG* 3.8 22.7 - - + +
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Residues in contact with LEU 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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98A ILE* 3.5 15.9 - - + +
100A ALA* 4.2 7.2 - - + -
110A ALA 4.0 20.2 - - - +
111A GLY* 3.9 14.8 - - - +
114A ALA* 4.0 14.8 - - + -
121A ILE 3.5 1.2 + - - -
122A ALA* 1.3 75.5 - - - +
124A ILE* 1.3 70.1 + - - +
125A HIS* 3.6 37.5 - - + +
142A GLN* 4.2 10.3 - - - +
157A TYR* 4.2 14.1 - - + -
158A PRO 5.2 0.2 + - - -
159A PRO* 3.2 22.2 - - + +
160A ARG* 2.9 29.5 + - - +
161A PHE 3.8 0.5 + - - -
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Residues in contact with ILE 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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29A ILE* 4.0 17.5 - - + -
34A PHE* 4.2 8.7 - - + -
37A TYR* 3.9 19.5 - - + -
57A PHE* 4.0 14.4 - - + -
97A ALA* 3.8 24.9 - - + -
98A ILE 2.8 13.8 + - - +
99A VAL* 3.4 9.3 - - + -
100A ALA* 2.8 28.9 + - - +
122A ALA* 5.1 0.4 - - + -
123A LEU* 1.3 78.7 - - - +
125A HIS* 1.3 65.5 + - - +
160A ARG* 5.0 2.7 - - + -
161A PHE* 3.3 20.2 - - + +
163A PHE* 3.8 29.8 - - + -
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Residues in contact with HIS 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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100A ALA* 3.9 21.8 - - + -
107A GLY* 3.8 25.6 + - - -
123A LEU* 3.6 31.2 - - + +
124A ILE* 1.3 72.0 - - - +
126A VAL* 1.3 59.6 + - - +
127A PRO* 3.5 3.2 - - + +
136A SER 5.9 0.2 - - - -
137A VAL* 3.8 39.3 - - + +
139A SER 5.8 2.7 - - - -
142A GLN* 4.6 9.4 - - - -
159A PRO* 3.9 20.7 - - + +
161A PHE 2.9 9.1 + - - -
162A VAL* 3.4 12.3 - - + +
163A PHE* 2.8 32.7 + - - -
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Residues in contact with VAL 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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22A LEU* 4.1 20.9 - - + -
49A ILE* 5.6 2.0 - - + -
53A ALA* 4.9 1.6 - - + -
57A PHE* 4.0 19.7 - - + -
99A VAL* 3.5 25.4 - - + -
100A ALA 2.8 15.8 + - - +
101A VAL* 3.9 20.9 - - + -
102A GLY 3.3 19.8 + - - -
124A ILE* 3.8 1.5 + - + -
125A HIS* 1.3 79.0 - - - +
127A PRO* 1.3 66.4 - - - +
128A THR* 3.4 7.5 + - + +
163A PHE* 3.5 15.7 - - + +
165A ASP* 5.8 4.3 - - + +
168A ILE* 5.9 4.7 - - + -
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Residues in contact with PRO 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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102A GLY 3.2 8.5 - - - +
125A HIS* 3.5 8.5 - - + +
126A VAL* 1.3 88.2 - - - +
128A THR* 1.3 62.1 + - - +
129A THR 3.5 1.1 - - - -
132A ALA* 3.8 10.5 - - + -
133A ALA* 3.5 39.9 - - + +
137A VAL* 3.9 16.8 - - + -
162A VAL* 3.9 11.2 - - + -
163A PHE 3.2 18.5 - - - +
164A ALA* 4.2 11.9 - - + -
165A ASP 4.8 2.4 + - - +
168A ILE* 5.3 1.2 - - - +
169A LEU* 3.8 10.6 - - - +
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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