Contacts of the strand formed by residues 118 - 123 (chain A) in PDB entry 6GES
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 VAL 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71A LYS 3.4 1.9 - - - +
72A LYS* 3.5 2.1 - - - +
73A ILE* 2.8 40.7 + - + +
75A PRO* 5.1 2.5 - - + -
76A PHE* 3.5 27.1 - - + -
85A THR* 5.2 5.4 - - + -
89A ILE* 4.6 7.9 - - + -
106A ILE* 3.4 28.0 - - + -
107A LEU 3.6 6.3 - - - +
108A ARG* 4.4 2.9 - - + -
115A MET* 4.3 7.6 - - - -
117A ASP* 1.3 79.8 - - - +
119A TYR* 1.3 67.3 + - - +
120A ILE* 4.6 8.3 - - + -
364A ILE* 4.2 12.3 - - + -
368A THR* 4.5 9.0 - - + -
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Residues in contact with TYR 119 (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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35A PRO* 3.5 11.8 + - - +
36A PHE* 3.9 11.7 - + - -
37A ASP* 3.0 39.5 + - + +
38A VAL* 3.5 23.1 - - + -
70A ILE* 3.9 17.5 - - + -
71A LYS 3.2 3.4 - - - -
72A LYS* 3.4 44.6 + - + -
106A ILE* 3.2 7.8 - - - +
107A LEU* 2.9 58.8 + - + +
108A ARG* 5.4 1.8 - - - -
117A ASP* 3.6 20.0 + - - -
118A VAL* 1.3 76.7 - - - +
120A ILE* 1.3 62.0 + - - +
121A VAL 4.0 0.6 + - - -
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Residues in contact with ILE 120 (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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69A ALA 3.7 0.5 - - - +
70A ILE* 3.3 3.0 - - - -
71A LYS* 2.8 42.5 + - + +
73A ILE* 3.4 32.1 - - + -
88A GLU* 4.1 15.5 - - + +
89A ILE* 4.0 25.1 - - + -
92A LEU* 6.1 0.4 - - + -
103A ILE* 3.8 34.3 - - + -
105A ASP 3.8 2.7 - - - -
106A ILE* 4.7 7.0 - - + +
118A VAL* 4.6 11.0 - - + -
119A TYR* 1.3 74.5 - - - +
121A VAL* 1.3 63.1 + - - +
122A GLN* 3.9 20.9 + - + +
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Residues in contact with VAL 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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42A TYR* 3.9 18.6 - - + +
61A ASP* 5.8 0.2 - - - +
64A ARG* 5.7 0.4 - - - +
68A VAL* 3.7 27.6 - - + -
69A ALA 3.4 9.0 - - - +
70A ILE* 4.2 12.8 - - + -
103A ILE* 3.6 2.1 - - - +
104A ARG* 2.7 42.3 + - + -
105A ASP* 2.9 27.8 + - + +
107A LEU* 3.6 31.0 - - + -
120A ILE* 1.3 72.6 - - - +
122A GLN* 1.3 64.9 + - - +
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Residues in contact with GLN 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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68A VAL* 3.6 7.1 - - - +
69A ALA* 2.8 37.7 + - + +
71A LYS* 4.0 25.4 - - - +
88A GLU* 5.5 0.8 + - - -
92A LEU* 4.0 12.9 - - - +
101A ILE* 3.6 30.3 - - + +
102A GLY 3.3 23.2 + - - +
104A ARG* 3.9 10.3 - - - -
120A ILE* 3.9 21.9 - - + +
121A VAL* 1.3 81.4 - - - +
123A ASP* 1.4 61.3 - - - +
124A LEU 3.4 0.2 + - - -
183A CYS* 5.6 0.6 - - - +
401A 6H3 2.9 27.5 - - + +
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Residues in contact with ASP 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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64A ARG* 4.9 2.3 + - - +
68A VAL* 5.3 2.9 - - - +
101A ILE* 4.0 16.1 - - + +
102A GLY* 4.9 6.6 + - - -
104A ARG* 2.4 44.7 + - - +
122A GLN* 1.4 74.9 - - - +
124A LEU* 1.3 65.5 + - - +
125A MET* 3.4 12.8 + - - +
181A LYS* 4.3 17.0 + - - +
401A 6H3 3.3 18.0 - - - -
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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