Contacts of the helix formed by residues 119 - 128 (chain B) in PDB entry 4L6V
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 119 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO* 6.5 0.4 - - - -
116B ALA* 5.0 2.6 - - - +
117B TYR* 3.2 5.5 - - - +
118B SER* 1.3 77.5 + - - +
120B VAL* 1.3 62.8 + - - +
121B TYR* 3.3 3.6 - - - -
122B HIS* 3.3 31.5 + - - +
123B TRP* 3.3 10.7 + - - +
356B TYR* 5.4 1.0 - - - -
359B ILE* 4.6 5.7 - - - +
365B THR* 3.9 17.6 - - - +
369B LEU* 4.5 5.1 - - - +
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Residues in contact with VAL 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 5.5 13.7 - - + +
68B VAL* 4.8 7.4 - - + -
116B ALA* 5.5 2.5 - - + -
118B SER* 3.3 32.8 - - - +
119B GLY* 1.3 75.4 - - - +
121B TYR* 1.3 78.0 + - + +
122B HIS 3.1 0.4 - - - -
123B TRP* 3.1 17.8 + - + +
124B PHE* 2.8 62.4 + - + -
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Residues in contact with TYR 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 3.6 27.0 - - + +
72B GLY* 3.3 21.7 - - - -
73B ASN* 3.4 7.3 + - - -
74B PHE* 3.5 38.3 - + + -
77B TRP* 3.4 33.1 - + + -
86B PRO* 3.4 30.3 - - + -
87B ILE 2.5 38.6 + - - -
116B ALA* 4.5 7.6 - - + -
119B GLY* 5.0 0.7 - - - -
120B VAL* 1.3 92.1 - - + +
122B HIS* 1.3 64.4 + - + +
124B PHE* 4.5 5.4 - + - -
125B TYR* 3.2 26.2 + - - +
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Residues in contact with HIS 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B TRP* 3.3 35.8 - + - -
81B PRO 5.2 2.2 + - - -
86B PRO* 4.9 5.2 - - + -
119B GLY* 3.5 26.6 + - - +
120B VAL 3.1 0.4 - - - -
121B TYR* 1.3 78.2 - - + +
123B TRP* 1.3 61.0 + - - +
125B TYR* 4.1 1.3 - - - +
126B THR* 2.5 34.8 + - - -
356B TYR* 3.9 15.7 - - + -
357B ALA 3.2 25.1 - - - +
358B PHE 3.5 10.8 + - - -
359B ILE* 3.4 22.8 - - + +
362B ASP* 3.7 28.0 + - + +
365B THR* 4.5 4.0 - - + -
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Residues in contact with TRP 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B THR* 6.3 4.9 - - + -
119B GLY 3.3 9.1 + - - +
120B VAL* 3.1 18.5 + - + +
122B HIS* 1.3 76.9 - - - +
124B PHE* 1.3 94.1 + + - +
126B THR* 3.3 2.3 + - - -
127B ILE* 3.2 49.2 + - + +
190B TRP* 5.0 6.4 - + - -
356B TYR* 3.3 41.7 + + + -
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Residues in contact with PHE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 4.9 8.3 - - - -
65B LEU* 3.4 39.5 - - + -
68B VAL* 4.9 11.0 - - + -
74B PHE* 4.1 8.7 - + + -
120B VAL* 2.8 49.3 + - + +
121B TYR* 4.1 6.5 - - - +
123B TRP* 1.3 105.7 - + - +
125B TYR* 1.3 62.7 + - - +
127B ILE* 3.2 16.0 - - + +
129B MET* 2.9 48.7 + - + +
135B LEU* 3.9 18.4 - - + -
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Residues in contact with TYR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B PHE* 4.2 6.0 - - + -
77B TRP* 3.8 21.1 - + + -
78B ILE* 3.7 42.1 + - + +
81B PRO* 5.0 2.0 - - + -
121B TYR 3.2 17.3 + - - +
122B HIS 4.1 2.5 - - - +
124B PHE* 1.3 78.3 - - - +
126B THR* 1.3 63.8 + - - +
127B ILE 3.4 0.5 + - - -
128B GLY* 3.4 12.1 + - - -
129B MET 3.7 15.2 - - - +
130B THR* 6.0 3.1 - - + -
201B GLU 6.1 1.3 - - - -
244B PHE* 3.7 41.3 + + - -
245B GLY* 4.1 7.8 - - - -
357B ALA* 4.8 4.3 - - + -
358B PHE* 3.7 31.3 - + - -
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Residues in contact with THR 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B HIS 2.5 23.9 + - - -
123B TRP 3.7 3.6 - - - -
124B PHE 3.3 0.4 - - - -
125B TYR* 1.3 79.4 - - - +
127B ILE* 1.3 63.5 + - + +
128B GLY 3.6 0.3 + - - -
194B LEU* 5.9 0.2 - - - +
198B ALA* 3.9 12.8 - - - +
244B PHE* 4.3 14.0 - - + -
267B SER* 5.6 1.3 - - - +
270B LEU* 3.7 32.6 - - + +
355B SER 3.5 21.3 - - - +
356B TYR* 3.7 7.8 - - + -
357B ALA* 3.1 26.0 + - + +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 3.2 45.7 + - + +
124B PHE* 3.2 23.6 - - + +
126B THR* 1.3 80.2 - - + +
128B GLY* 1.3 56.1 + - - +
129B MET* 4.3 17.0 - - + -
190B TRP* 3.5 38.8 - - + -
193B HIS* 3.2 27.4 - - + -
194B LEU* 5.5 2.9 - - + -
197B VAL* 4.3 0.3 - - - +
198B ALA* 3.3 19.1 + - - +
356B TYR* 5.4 1.3 - - + -
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Residues in contact with GLY 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B PHE 3.3 1.0 + - - -
125B TYR 3.4 5.3 + - - -
126B THR 3.3 3.8 - - - -
127B ILE* 1.3 79.8 - - - +
129B MET* 1.3 67.5 + - - +
130B THR* 3.2 1.7 + - - -
134B GLU* 3.6 5.0 - - - +
197B VAL* 4.6 10.6 - - - +
198B ALA* 4.4 9.2 - - - -
201B GLU* 3.1 32.5 - - - +
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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