Contacts of the helix formed by residues 116 - 128 (chain B) in PDB entry 6FF8
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 ALA 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B GLU* 3.2 43.7 - - + +
87B ARG* 4.3 8.5 - - - +
112B SER 3.2 13.3 + - - +
113B THR 3.8 2.2 - - - +
114B PHE 3.2 1.0 - - - -
115B GLU* 1.3 76.1 - - - +
117B VAL* 1.3 63.8 + - - +
118B LEU 3.2 0.4 - - - -
119B LYS* 3.0 24.4 + - - +
120B TRP* 3.1 16.3 + - + -
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Residues in contact with VAL 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 4.1 15.7 - - + +
105B VAL 4.9 2.5 - - - +
106B PHE* 4.1 18.6 - - + -
113B THR 3.5 11.3 + - - +
114B PHE* 3.1 20.8 + - + +
116B ALA* 1.3 76.2 - - - +
118B LEU* 1.3 53.6 + - + +
120B TRP* 3.5 5.3 + - - +
121B LYS* 2.8 32.2 + - - +
140B LEU* 3.9 16.4 - - + -
161B PHE* 3.7 26.7 - - + -
167B PHE* 3.8 22.9 - - + -
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Residues in contact with LEU 118 (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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114B PHE* 4.1 7.4 - - + +
115B GLU* 3.7 18.2 - - - +
116B ALA 3.2 0.4 - - - -
117B VAL* 1.3 76.9 - - + +
119B LYS* 1.3 55.1 + - + +
121B LYS* 4.2 7.2 - - + -
122B SER* 2.6 40.6 + - - -
161B PHE* 3.5 40.8 - - + -
165B HIS* 3.5 35.4 - - + +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B ARG* 3.6 42.5 - - - +
115B GLU* 4.5 5.9 + - - +
116B ALA* 3.0 19.9 + - - +
118B LEU* 1.3 77.4 - - + +
120B TRP* 1.3 62.3 + - - +
122B SER* 3.1 8.3 + - - -
123B ASP* 3.1 24.0 + - - +
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Residues in contact with TRP 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE* 3.7 34.7 - - + +
32B GLY* 3.3 42.0 - - - -
33B GLU* 2.7 23.5 + - + -
82B ILE* 4.4 10.1 - - + -
83B ALA 3.9 15.9 - - - -
84B GLY 3.4 17.5 - - - -
86B GLU 4.2 0.2 - - - -
87B ARG* 3.6 43.5 - - + +
92B THR* 4.7 1.8 - - + -
96B TYR* 3.6 24.9 - - - -
104B VAL* 4.4 6.1 - - + -
116B ALA* 3.1 25.5 + - + -
117B VAL* 3.7 7.9 - - - +
119B LYS* 1.3 75.8 - - - +
121B LYS* 1.3 57.4 + - - +
123B ASP* 3.2 6.1 + - - +
124B LEU* 3.0 30.0 + - - +
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Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 4.8 4.2 - - + +
117B VAL 2.8 21.5 + - - +
118B LEU* 4.0 9.9 - - + +
119B LYS 3.4 0.2 - - - -
120B TRP* 1.3 74.2 - - - +
122B SER* 1.3 57.0 + - - +
124B LEU* 3.4 18.6 + - + +
125B ASP* 2.7 55.8 + - - +
135B PRO* 5.8 1.8 - - - +
136B ILE 5.6 0.9 + - - -
138B ALA* 3.7 18.8 - - + -
165B HIS 3.0 23.4 + - - +
166B GLY* 3.3 23.9 + - - -
167B PHE* 3.8 31.6 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU 2.6 28.6 + - - -
119B LYS* 3.1 14.0 + - - -
121B LYS* 1.3 70.8 - - - +
123B ASP* 1.3 56.2 + - - -
125B ASP* 3.5 4.5 + - - +
126B SER* 3.0 31.2 + - - -
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Residues in contact with ASP 123 (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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87B ARG* 4.7 15.0 - - + +
92B THR* 3.0 20.2 + - - +
96B TYR* 2.6 25.4 + - - +
119B LYS 3.1 15.6 + - - +
120B TRP* 3.4 14.9 - - + +
122B SER* 1.3 74.9 + - - +
124B LEU* 1.3 62.6 + - - +
126B SER* 3.4 4.8 + - - -
127B LYS* 2.8 56.5 + - - +
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Residues in contact with LEU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 3.5 31.9 - - + -
31B ILE* 4.1 21.8 - - + -
96B TYR* 3.8 13.0 - - + -
102B ALA* 3.9 19.5 - - + -
104B VAL* 4.7 2.5 - - + -
120B TRP 3.0 14.7 + - - +
121B LYS* 3.4 23.8 - - + +
123B ASP* 1.3 76.2 - - - +
125B ASP* 1.3 68.8 + - - +
127B LYS* 3.1 1.9 + - - -
128B VAL* 3.1 35.9 + - + +
136B ILE* 4.1 17.3 - - + -
138B ALA* 4.5 8.3 - - + -
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Residues in contact with ASP 125 (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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121B LYS* 2.7 52.2 + - - +
122B SER* 4.4 4.0 - - - +
124B LEU* 1.3 86.8 - - - +
126B SER* 1.3 60.9 + - - +
127B LYS 3.5 0.3 + - - -
128B VAL 4.0 11.2 + - - +
129B HIS* 5.9 1.4 - - - +
135B PRO* 4.5 24.2 - - + +
136B ILE* 4.8 8.7 + - - +
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Residues in contact with SER 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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93B ARG* 3.7 18.7 + - - -
122B SER 3.0 19.1 + - - -
123B ASP* 3.6 8.1 - - - -
124B LEU 3.2 0.2 - - - -
125B ASP* 1.3 75.8 - - - +
127B LYS* 1.3 67.9 + - - +
129B HIS* 5.9 1.8 - - - -
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B THR* 3.4 22.6 + - - +
93B ARG* 3.7 67.7 + - + +
96B TYR* 3.7 15.4 - - + +
97B LYS* 5.9 0.9 + - - -
123B ASP* 2.8 41.3 + - - +
124B LEU 3.1 1.6 + - - -
126B SER* 1.3 86.5 - - - +
128B VAL* 1.3 62.6 + - - +
129B HIS* 5.2 3.9 - - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.9 0.7 - - + -
96B TYR* 3.6 40.6 - - + +
97B LYS* 4.8 1.3 - - - -
98B GLU 4.4 6.3 - - - +
99B ALA 3.8 20.4 - - - +
124B LEU* 3.1 32.3 + - + +
125B ASP* 4.0 12.0 - - - +
126B SER 3.8 0.6 - - - -
127B LYS* 1.3 81.2 - - - +
129B HIS* 1.3 74.7 + - - +
135B PRO* 5.2 1.9 - - - +
136B ILE* 4.1 20.6 + - + +
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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