Contacts of the strand formed by residues 118 - 123 (chain D) in PDB entry 3GXM
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 ILE 118 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79D LYS* 4.1 17.3 - - + +
80D GLY* 3.6 10.1 - - - -
81D PHE* 3.1 31.1 + - - +
82D GLY* 3.3 19.8 - - - +
83D GLY 3.5 3.2 + - - -
109D PHE* 4.4 4.7 - - - -
116D TYR 3.7 0.4 - - - -
117D ASN* 1.3 84.5 - - - +
119D ILE* 1.3 76.3 + - - +
120D ARG 4.7 0.7 - - - +
172D VAL* 4.0 0.4 - - - +
173D SER* 3.3 14.1 - - - +
175D LEU* 4.8 5.6 - - + -
228D TRP* 4.5 10.1 - - + -
337D PHE* 3.8 32.3 - - + -
379D THR* 4.1 22.0 - - + +
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Residues in contact with ILE 119 (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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83D GLY 3.4 8.3 - - - +
85D MET* 3.8 31.6 - - + +
109D PHE* 3.6 33.0 - - + -
118D ILE* 1.3 81.1 - - - +
120D ARG* 1.3 63.4 + - - +
121D VAL* 3.9 11.1 + - + +
161D ILE* 4.2 16.6 - - + -
164D ALA* 4.0 17.0 - - + -
165D LEU* 4.3 1.1 - - + -
172D VAL* 4.0 10.5 - - + +
173D SER 3.0 7.4 + - - -
174D LEU* 3.3 23.9 - - + -
175D LEU 2.9 22.7 + - - +
383D LEU* 4.9 3.4 - - + -
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Residues in contact with ARG 120 (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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83D GLY 3.1 8.1 + - - +
84D ALA* 3.4 17.1 - - + +
85D MET* 2.9 26.9 + - - -
118D ILE* 4.2 1.6 - - - +
119D ILE* 1.3 73.0 - - - +
121D VAL* 1.3 64.3 + - - +
122D PRO* 3.8 3.5 - - + +
175D LEU* 3.3 32.8 - - + +
177D SER* 3.1 24.0 + - - +
179D TRP* 3.6 8.7 - - + -
234D ASN* 2.8 24.4 + - - -
282D ASP* 3.0 26.8 + - - -
311D HIS* 4.0 0.4 - - - -
339D SER 3.3 27.3 + - - -
340D GLU* 3.0 28.7 + - - +
379D THR* 4.3 10.5 - - + -
380D ASP 5.7 0.2 - - - -
381D TRP* 3.9 13.7 - - + -
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Residues in contact with VAL 121 (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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85D MET* 4.6 1.3 - - + +
119D ILE* 4.0 15.5 - - + +
120D ARG* 1.3 78.3 - - - +
122D PRO* 1.4 72.6 - - - +
123D MET 3.5 0.5 + - - -
157D LYS* 3.9 9.9 - - - -
161D ILE* 3.8 24.7 - - + -
174D LEU* 4.7 4.5 - - + -
175D LEU 2.7 8.5 + - - -
176D ALA* 3.2 22.7 - - - +
177D SER 3.3 2.9 + - - -
216D PHE* 4.4 3.1 - - + -
220D TYR* 3.7 31.4 - - + +
227D PHE* 3.7 28.9 - - + -
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Residues in contact with PRO 122 (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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84D ALA* 5.3 0.2 - - + -
85D MET 3.3 23.1 - - - +
86D THR* 4.1 23.6 - - + -
87D ASP* 5.9 0.9 - - - +
120D ARG* 3.8 6.7 - - + +
121D VAL* 1.4 86.2 - - - +
123D MET* 1.3 59.8 + - - +
124D ALA 3.3 15.7 + - - +
126D CYS* 4.4 9.4 - - - -
135D TYR* 3.7 2.1 + - - -
157D LYS* 2.7 33.3 + - - +
177D SER 3.4 7.4 - - - +
179D TRP* 3.7 29.6 - - + -
216D PHE* 4.7 0.2 - - - -
381D TRP* 4.6 3.1 - - + -
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Residues in contact with MET 123 (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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122D PRO* 1.3 67.5 - - - +
124D ALA* 1.3 68.9 + - - +
125D SER 3.9 1.2 + - - +
135D TYR* 3.6 12.8 - - + -
176D ALA* 3.9 28.0 - - + -
177D SER* 2.9 11.3 + - - -
178D PRO* 3.6 53.7 - - + +
179D TRP* 4.1 5.9 + - - -
180D THR 4.8 4.0 + - - +
212D TYR* 4.0 29.4 + - + -
213D PHE* 4.1 32.8 - - + -
216D PHE* 3.9 23.8 - - + -
230D VAL* 5.2 1.1 - - - -
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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