Contacts of the strand formed by residues 124 - 131 (chain A) in PDB entry 1GN6
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 GLY 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A VAL* 3.8 9.5 - - - +
122A GLY 3.9 1.4 + - - -
123A SER* 1.3 75.1 - - - +
125A TRP* 1.3 67.3 + - - -
142A VAL 3.0 14.8 - - - -
144A ASP 3.8 9.0 - - - -
161A MET* 2.8 33.9 + - - -
162A TRP* 3.5 7.3 + - - -
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Residues in contact with TRP 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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75A ASN* 3.3 56.7 - - + +
76A HIS* 3.8 26.9 - + - -
79A TRP* 4.1 9.9 - + + -
120A VAL* 4.5 6.1 - - - +
124A GLY* 1.3 75.9 - - - -
126A ALA* 1.3 64.7 + - - +
141A GLN* 3.8 7.3 - - - +
142A VAL* 3.0 42.8 + - + +
144A ASP 3.1 20.8 + - - -
145A HIS* 3.0 22.7 + + - -
158A LEU* 3.8 25.6 - - + -
159A LEU 3.1 10.5 - - - -
160A ASP* 3.3 49.4 - - + -
161A MET* 4.1 4.0 - - - +
162A TRP* 3.9 2.6 - - - +
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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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113A PHE* 3.9 26.3 - - + +
116A ALA* 4.2 8.3 - - + -
117A ALA* 3.7 38.0 - - + +
125A TRP* 1.3 75.2 - - - +
127A ALA* 1.3 62.5 + - - +
139A ILE* 5.2 0.2 - - + -
140A PHE 3.8 2.9 - - - -
141A GLN* 4.9 0.9 - - - +
158A LEU* 3.4 4.9 - - - +
159A LEU* 3.0 30.1 + - + +
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Residues in contact with ALA 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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113A PHE* 4.0 4.7 - - - -
126A ALA* 1.3 75.8 - - - +
128A LEU* 1.3 61.3 + - - +
129A GLY* 3.9 0.8 + - - +
138A LEU 3.8 0.3 - - - +
139A ILE* 3.2 5.7 - - - +
140A PHE* 2.7 50.9 + - + +
142A VAL* 4.1 15.7 - - + -
155A PRO* 5.8 0.7 - - + -
157A LEU 3.6 3.8 - - - -
158A LEU* 3.1 27.1 - - + -
151C LEU* 5.1 7.9 - - + -
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Residues in contact with LEU 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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95A LEU* 5.2 1.3 - - + -
99A ILE* 4.8 13.2 - - + -
103A PHE* 3.8 20.9 - - + -
109A PHE* 3.8 31.2 - - + -
113A PHE* 3.8 10.2 - - + -
127A ALA* 1.3 71.6 - - - +
129A GLY* 1.3 59.9 + - - +
137A LEU* 4.1 12.6 - - + -
138A LEU 3.7 14.6 - - - +
139A ILE* 4.1 2.7 - - + +
155A PRO* 3.7 1.9 - - - +
156A LEU* 2.7 52.7 + - + -
157A LEU* 3.0 28.9 + - + +
187A TRP* 5.6 0.4 - - + -
190A VAL* 4.6 9.2 - - + -
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Residues in contact with GLY 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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127A ALA* 3.9 2.4 + - - -
128A LEU* 1.3 75.9 - - - +
130A TRP* 1.3 61.6 + - - -
131A ASP 4.0 0.2 + - - -
137A LEU* 3.5 10.0 - - - +
138A LEU* 2.9 35.3 + - - +
140A PHE* 4.5 5.5 - - - -
153A ILE* 4.1 15.3 - - - -
154A VAL 3.3 10.8 - - - -
155A PRO* 4.3 1.3 - - - -
156A LEU* 4.3 1.8 - - - -
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Residues in contact with TRP 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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129A GLY* 1.3 74.4 - - - -
131A ASP* 1.3 63.2 + - - +
132A THR* 3.4 26.7 + - + +
135A ASN* 3.2 47.8 - - + +
136A LYS* 3.4 22.7 - - - -
137A LEU* 3.9 18.2 - - + -
153A ILE* 3.7 6.5 - - - +
154A VAL* 2.9 36.2 + - + +
156A LEU* 4.5 8.3 - - + +
194A TYR* 4.5 8.7 - + + -
197A ALA* 3.2 42.6 + - + -
198A THR* 3.7 31.8 - - + +
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Residues in contact with ASP 131 (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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129A GLY 4.0 1.0 + - - -
130A TRP* 1.3 72.9 - - - +
132A THR* 1.3 54.3 + - - +
133A LEU* 3.1 16.8 + - - +
134A GLY* 2.7 22.3 + - - -
135A ASN* 2.7 37.2 + - - -
136A LYS 2.7 20.6 + - - +
138A LEU* 3.8 18.1 - - + +
153A ILE* 3.8 15.5 - - + +
4C TYR* 2.7 25.4 + - - -
70C LEU* 4.4 11.7 - - - +
74C VAL* 4.9 4.3 - - - +
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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