Contacts of the strand formed by residues 124 - 131 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D VAL* 3.8 8.9 - - - +
122D GLY 3.9 1.6 + - - -
123D SER* 1.3 76.3 - - - +
125D TRP* 1.3 66.3 + - - -
142D VAL 3.0 14.4 - - - -
144D ASP 3.8 9.4 - - - -
161D MET* 2.8 34.4 + - - -
162D TRP* 3.5 7.3 + - - -
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Residues in contact with TRP 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ASN* 3.3 55.8 - - + +
76D HIS* 3.8 28.0 - + - -
79D TRP* 4.1 9.4 - + + -
120D VAL* 4.5 5.9 - - - +
124D GLY* 1.3 75.8 - - - -
126D ALA* 1.3 64.3 + - - +
141D GLN* 3.8 7.4 - - - +
142D VAL* 3.0 42.9 + - + +
144D ASP 3.1 20.3 + - - -
145D HIS* 3.0 22.9 + + - -
158D LEU* 3.8 22.9 - - + -
159D LEU 3.1 11.2 - - - -
160D ASP* 3.3 49.6 - - + -
161D MET* 4.1 4.0 - - - +
162D TRP* 3.9 2.4 - - - +
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Residues in contact with ALA 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D PHE* 3.9 26.3 - - + +
116D ALA* 4.2 7.9 - - + -
117D ALA* 3.7 38.5 - - + +
125D TRP* 1.3 75.0 - - - +
127D ALA* 1.3 62.0 + - - +
139D ILE* 5.2 0.2 - - + -
140D PHE 3.8 2.9 - - - -
141D GLN* 4.9 0.9 - - - +
158D LEU* 3.4 5.0 - - - +
159D LEU* 3.0 30.3 + - + +
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Residues in contact with ALA 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B LEU* 5.1 7.4 - - + -
113D PHE* 4.0 6.2 - - - -
126D ALA* 1.3 76.4 - - - +
128D LEU* 1.3 60.0 + - - +
129D GLY* 3.9 1.2 + - - +
138D LEU 3.8 0.3 - - - +
139D ILE* 3.2 6.6 - - - +
140D PHE* 2.7 50.4 + - + +
142D VAL* 4.1 16.4 - - + -
155D PRO* 5.8 0.9 - - + -
157D LEU 3.6 3.1 - - - -
158D LEU* 3.1 26.7 - - + -
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Residues in contact with LEU 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D LEU* 5.2 0.9 - - + -
99D ILE* 4.8 13.2 - - + -
103D PHE* 3.8 20.4 - - + -
109D PHE* 3.8 31.2 - - + -
113D PHE* 3.8 10.2 - - + -
127D ALA* 1.3 72.4 - - - +
129D GLY* 1.3 59.5 + - - +
137D LEU* 4.1 13.0 - - + -
138D LEU 3.7 15.3 - - - +
139D ILE* 4.1 2.5 - - + +
155D PRO* 3.7 2.1 - - - +
156D LEU* 2.7 51.8 + - + -
157D LEU* 3.0 29.6 + - + +
187D TRP* 5.6 0.2 - - + -
190D VAL* 4.6 9.6 - - + -
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Residues in contact with GLY 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D ALA* 3.9 2.0 + - - -
128D LEU* 1.3 76.4 - - - +
130D TRP* 1.3 60.7 + - - -
131D ASP 4.0 0.4 + - - -
137D LEU* 3.5 10.1 - - - +
138D LEU 2.9 36.3 + - - -
140D PHE* 4.5 5.2 - - - -
153D ILE* 4.1 15.3 - - - -
154D VAL 3.3 11.0 - - - -
155D PRO* 4.3 1.3 - - - -
156D LEU* 4.3 1.3 - - - -
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Residues in contact with TRP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D GLY* 1.3 75.0 - - - -
131D ASP* 1.3 64.4 + - - +
132D THR* 3.4 25.8 + - + +
135D ASN* 3.2 47.6 - - + +
136D LYS* 3.4 21.8 - - - -
137D LEU* 3.9 17.9 - - + -
153D ILE* 3.7 6.2 - - - -
154D VAL* 2.9 36.7 + - + +
156D LEU* 4.5 8.3 - - + +
194D TYR* 4.5 9.9 - + + -
197D ALA* 3.2 41.3 + - + -
198D THR* 3.7 29.8 - - + -
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Residues in contact with ASP 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B TYR* 2.7 26.8 + - - +
70B LEU* 4.4 11.2 - - - +
74B VAL* 5.0 4.0 - - - +
129D GLY 4.0 1.0 + - - -
130D TRP* 1.3 72.3 - - - +
132D THR* 1.3 54.5 + - - +
133D LEU* 3.1 16.6 + - - +
134D GLY* 2.7 22.3 + - - -
135D ASN* 2.7 37.8 + - - -
136D LYS 2.7 20.9 + - - +
138D LEU* 3.8 18.3 - - + +
153D ILE* 3.8 16.5 - - + +
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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