Contacts of the helix formed by residues 118 - 127 (chain B) in PDB entry 4FE1
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 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ALA* 5.2 1.6 + - - +
116B TYR* 3.2 5.1 + - - +
117B SER* 1.3 78.2 + - - +
119B VAL* 1.3 63.8 + - - +
120B TYR 3.3 2.9 - - - -
121B HIS* 3.3 26.3 + - - +
122B TRP* 3.2 19.7 + - - +
361B TYR* 5.1 1.7 - - - -
364B ILE* 4.6 11.0 - - - +
370B THR* 4.1 11.5 - - - +
374B LEU* 4.8 2.2 - - - -
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Residues in contact with VAL 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B SER* 5.3 9.4 - - - +
67B VAL* 4.4 7.0 - - + -
115B ALA* 5.2 4.3 - - + -
117B SER* 3.2 31.0 - - - +
118B GLY* 1.3 75.9 - - - +
120B TYR* 1.3 78.3 + - + +
122B TRP* 3.2 17.8 + - + +
123B TRP* 2.9 65.8 + - + -
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Residues in contact with TYR 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B VAL* 3.5 31.2 - - + +
71B GLY* 3.6 0.5 - - - -
72B ASN* 3.2 31.0 + - - -
73B PHE* 3.6 37.3 - + - -
76B TRP* 3.6 38.1 - + + -
85B PRO* 3.7 22.4 - - + -
86B ILE 2.7 39.2 + - - -
115B ALA* 4.4 5.6 - - + -
118B GLY 3.3 0.8 - - - -
119B VAL* 1.3 84.2 - - + +
121B HIS* 1.3 61.1 + - + +
123B TRP* 3.9 1.3 - + - -
124B TYR* 2.9 33.1 + - - +
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Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B TRP* 3.6 29.9 + + - -
80B PRO 5.3 2.9 - - - -
85B PRO* 5.0 4.0 - - + +
118B GLY* 3.5 26.0 - - - +
120B TYR* 1.3 81.9 - - + +
122B TRP* 1.3 56.2 + - - +
124B TYR* 3.5 2.1 - - - +
125B THR* 2.8 34.1 + - - -
361B TYR* 3.8 20.6 - - + -
362B ALA 3.3 20.0 + - - +
363B PHE* 3.6 10.5 - - + -
364B ILE* 3.3 29.6 - - + -
367B ASP* 3.2 32.6 + - + +
370B THR* 4.4 2.2 - - + -
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Residues in contact with TRP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B VAL* 5.1 15.3 - - + -
118B GLY 3.2 10.0 + - - +
119B VAL* 3.6 18.8 - - + +
120B TYR 3.2 0.4 - - - -
121B HIS* 1.3 77.1 - - - +
123B TRP* 1.3 89.5 + + - +
125B THR* 3.2 2.3 + - - -
126B ILE* 2.9 60.7 + - + +
189B TRP* 5.2 3.9 - + - -
361B TYR* 3.5 42.5 + + + -
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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
----------------------------------------------------------
60B VAL* 5.2 4.2 - - + +
63B SER* 3.8 11.7 - - - -
64B LEU* 3.4 48.5 - - + +
67B VAL* 3.6 32.8 - - + -
73B PHE* 3.9 11.9 - + + -
119B VAL* 2.9 44.9 + - + +
120B TYR* 4.6 1.8 - - - -
122B TRP* 1.3 99.9 - + - +
124B TYR* 1.3 61.5 + - - +
126B ILE* 3.4 23.6 + - + +
127B GLY 3.2 4.3 + - - -
128B MET* 2.6 52.6 + - + +
134B LEU* 3.8 20.4 - - + -
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Residues in contact with TYR 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B PHE* 4.1 2.4 - - + -
76B TRP* 3.3 25.6 - + + -
77B VAL* 3.9 35.3 + - + -
80B PRO* 4.0 8.9 - - + +
120B TYR 2.9 20.1 + - - +
121B HIS 3.5 2.5 - - - +
123B TRP* 1.3 77.5 - - - +
125B THR* 1.3 61.3 + - - +
127B GLY 3.2 1.2 + - - -
128B MET 3.7 3.4 - - - -
129B ARG* 2.4 57.2 + - - +
243B PHE* 3.4 41.6 + + - -
244B GLY* 4.4 2.5 - - - -
362B ALA* 3.6 19.3 - - + -
363B PHE* 3.5 30.3 - + - -
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Residues in contact with THR 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 HIS 2.8 20.8 + - - -
122B TRP 3.2 5.4 + - - -
124B TYR* 1.3 77.7 - - - +
126B ILE* 1.3 64.1 + - + +
127B GLY 3.2 1.1 + - - -
129B ARG* 5.3 0.3 + - - -
193B LEU* 6.0 0.9 - - + -
197B ALA* 3.6 15.9 - - - +
243B PHE* 4.8 12.4 - - + -
269B LEU* 3.9 26.5 - - + +
272B MET* 4.7 4.3 - - + -
360B PRO 3.8 18.6 - - - +
361B TYR* 3.4 12.4 - - + -
362B ALA* 3.1 24.2 + - - +
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Residues in contact with ILE 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 TRP* 2.9 59.1 + - + +
123B TRP* 3.5 31.9 - - + +
124B TYR 3.3 0.2 - - - -
125B THR* 1.3 77.4 - - + +
127B GLY* 1.3 56.5 + - - +
128B MET* 3.9 14.8 - - + -
189B TRP* 3.7 33.7 - - + -
192B HIS* 3.1 24.6 + - - +
193B LEU* 5.2 1.1 - - + -
196B VAL* 4.1 0.5 - - - +
197B ALA* 3.8 14.5 + - - +
361B TYR* 5.5 0.4 - - + -
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Residues in contact with GLY 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B TYR 3.2 5.5 + - - -
125B THR 3.2 2.0 + - - -
126B ILE* 1.3 80.9 - - - +
128B MET* 1.3 67.8 + - - +
129B ARG* 3.4 20.9 + - - +
133B ASP* 4.2 3.6 - - - +
196B VAL* 4.3 6.5 - - - +
197B ALA* 4.4 2.9 - - - -
200B GLU* 3.8 30.5 - - - +
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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