Contacts of the helix formed by residues 132 - 148 (chain L) in PDB entry 2WSF
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 SER 132 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106L SER* 4.6 3.6 - - - -
107L PHE 3.7 2.2 - - - -
108L LYS* 2.4 63.2 + - - +
110L GLY* 4.3 7.3 + - - -
130L LEU 4.2 0.8 - - - -
131L GLN* 1.3 77.5 - - - +
133L ALA* 1.3 61.3 + - - +
134L ASP* 3.4 17.3 + - - +
135L GLY* 3.5 4.3 + - - -
136L TRP* 3.4 15.1 + - - +
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Residues in contact with ALA 133 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103L GLY 4.4 7.0 - - - +
106L SER* 3.6 25.2 - - - +
107L PHE* 2.6 27.5 + - - +
109L GLU* 3.7 8.7 - - - +
132L SER* 1.3 71.2 - - - +
134L ASP* 1.3 54.5 + - - +
135L GLY 2.7 12.8 + - - -
136L TRP* 3.1 13.8 + - - +
137L ALA* 3.1 15.1 + - - +
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Residues in contact with ASP 134 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ARG* 5.7 2.6 - - - +
48L ASN* 5.2 0.5 - - - +
108L LYS 4.8 0.8 + - - -
109L GLU* 5.2 6.4 + - - +
110L GLY 3.6 27.4 + - - +
111L GLU* 5.0 7.6 - - + +
112L PRO* 5.9 2.3 - - - +
132L SER* 3.3 13.7 + - - +
133L ALA* 1.3 76.3 - - - +
135L GLY* 1.3 55.8 - - - +
137L ALA* 4.8 9.8 - - - +
138L LYS* 3.7 19.2 + - - +
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Residues in contact with GLY 135 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48L ASN* 5.2 0.9 - - - -
49L PRO* 3.2 18.0 - - - +
131L GLN* 3.3 11.9 - - - -
132L SER* 3.8 4.3 - - - -
133L ALA 2.7 2.4 + - - -
134L ASP* 1.3 74.0 - - - +
136L TRP* 1.3 57.0 + - - +
137L ALA* 2.9 3.6 - - - +
138L LYS* 2.8 41.5 + - - +
139L PHE 3.1 5.9 + - - -
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Residues in contact with TRP 136 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691B ILE* 5.1 7.5 - - + +
99L LEU* 2.9 60.1 - - + -
100L THR* 4.8 2.5 - - - -
102L TYR* 3.3 30.4 - + + -
103L GLY* 3.3 31.2 - - - -
106L SER* 5.0 9.0 - - - -
131L GLN* 3.1 30.1 + - - +
132L SER 3.4 7.1 + - - +
133L ALA* 3.1 9.4 + - - +
135L GLY* 1.3 72.5 - - - +
137L ALA* 1.3 56.7 + - - +
139L PHE* 4.1 17.7 - + + -
140L THR* 3.1 41.2 + - + +
211L BCR 4.1 8.3 - - + -
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Residues in contact with ALA 137 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H PHE* 4.2 6.7 - - - +
50H ARG* 3.5 37.5 - - + +
133L ALA 3.1 13.9 + - - +
134L ASP* 4.8 9.4 - - - +
135L GLY 2.8 3.0 + - - +
136L TRP* 1.3 74.0 - - - +
138L LYS* 1.3 52.6 + - + +
139L PHE 3.0 5.1 + - - -
140L THR* 3.1 5.6 + - - -
141L GLY* 2.6 35.9 + - - -
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Residues in contact with LYS 138 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H PHE 4.8 7.6 + - - +
48H THR* 5.3 12.6 - - + -
48L ASN* 3.5 39.1 + - - +
49L PRO* 3.9 6.1 - - + -
50L LEU* 3.0 41.0 - - + +
111L GLU* 4.1 16.6 + - - -
112L PRO* 6.0 1.4 - - - +
113L SER* 5.8 3.0 - - - +
134L ASP* 3.7 12.6 + - - +
135L GLY* 2.8 39.9 + - - +
137L ALA* 1.3 75.0 - - + +
139L PHE* 1.3 55.7 + - - +
141L GLY* 4.0 2.7 - - - +
142L GLY* 3.4 11.1 + - - -
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Residues in contact with PHE 139 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41L PRO* 5.4 7.0 - - + -
49L PRO* 3.3 39.2 + - + -
52L ARG* 3.9 7.0 - - + -
53L GLY* 3.5 26.1 - - - -
56L VAL* 3.7 36.3 - - + -
99L LEU* 4.6 14.1 - - + -
135L GLY 3.1 6.3 + - - +
136L TRP* 4.3 21.5 - + + +
137L ALA 3.0 0.8 - - - -
138L LYS* 1.3 75.6 - - - +
140L THR* 1.3 64.4 + - + +
141L GLY 2.9 4.3 - - - -
142L GLY* 2.8 5.9 + - - -
143L PHE* 2.7 36.9 + + - +
209L CLA 5.8 3.1 - - + -
211L BCR 5.3 8.1 - - + -
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Residues in contact with THR 140 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47H PHE* 3.2 15.1 - - - -
96L SER* 4.9 5.8 + - - -
99L LEU* 3.6 29.8 - - + -
100L THR* 3.4 25.6 + - - +
136L TRP* 3.1 50.5 + - + +
137L ALA* 3.1 4.8 + - - -
139L PHE* 1.3 77.3 - - + +
141L GLY* 1.3 57.1 + - - +
143L PHE* 3.6 12.9 - - - +
144L PHE* 3.7 13.3 + - - +
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Residues in contact with GLY 141 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44H ALA* 5.9 0.9 - - - +
47H PHE* 3.1 35.2 - - - +
48H THR* 6.0 1.6 - - - -
137L ALA 2.6 19.0 + - - -
138L LYS* 4.3 2.2 - - - -
140L THR* 1.3 73.0 - - - +
142L GLY* 1.3 61.1 + - - +
143L PHE 3.1 1.5 + - - -
144L PHE* 3.7 9.9 + - - +
145L PHE* 3.7 12.8 + - - +
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Residues in contact with GLY 142 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50L LEU 4.3 2.9 - - - -
53L GLY* 3.4 14.5 - - - +
54L VAL* 3.3 23.2 - - - +
138L LYS 3.4 13.6 + - - -
139L PHE 2.8 11.0 + - - -
141L GLY* 1.3 72.3 - - - +
143L PHE* 1.3 57.7 + - - +
145L PHE* 2.8 25.5 - - - +
146L GLY* 3.7 0.3 + - - -
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Residues in contact with PHE 143 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53L GLY 3.8 5.8 + - - +
56L VAL* 4.6 12.6 - - + -
57L GLY* 4.0 24.2 - - - -
60L HIS* 5.0 8.3 - - + -
92L VAL* 3.8 20.2 - - + -
95L LEU* 3.2 35.9 - - + -
96L SER* 2.7 29.8 - - - -
99L LEU* 4.4 12.6 - - + -
139L PHE* 2.7 14.3 + + + +
140L THR* 3.7 23.1 - - - +
141L GLY 3.1 0.2 - - - -
142L GLY* 1.3 72.4 - - - +
144L PHE* 1.3 55.5 + - - +
147L GLY* 2.6 33.8 + - - -
203L CLA 6.5 1.1 - - + -
211L BCR 4.4 19.5 - - + -
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Residues in contact with PHE 144 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H PHE* 5.2 15.5 - + + -
57H LEU* 4.1 25.6 - - + -
92L VAL 4.8 0.2 - - - -
93L VAL* 3.9 26.7 - - + -
96L SER* 3.7 26.1 + - - +
140L THR 3.7 8.4 + - - +
141L GLY* 3.7 9.5 + - - +
142L GLY 3.5 0.4 - - - -
143L PHE* 1.3 74.7 - - - +
145L PHE* 1.3 60.3 + + + +
146L GLY 2.9 2.1 + - - -
148L VAL* 2.9 66.2 + - + +
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Residues in contact with PHE 145 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40H PHE* 6.4 2.2 - + - -
43H PHE* 4.6 10.3 - + - -
44H ALA* 2.6 43.3 - - + -
54L VAL* 3.1 18.5 - - + +
141L GLY 3.7 10.5 + - - +
142L GLY* 2.8 16.4 - - - +
143L PHE 3.5 0.2 - - - -
144L PHE* 1.3 76.1 - + + +
146L GLY* 1.3 54.8 + - - +
148L VAL 3.7 2.7 - - - -
149L SER* 3.5 30.5 - - - -
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Residues in contact with GLY 146 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54L VAL* 4.1 4.0 - - - -
57L GLY* 2.9 22.8 - - - +
58L LEU* 3.0 29.8 - - - -
61L GLY* 3.8 0.5 - - - -
142L GLY 3.9 0.7 - - - -
143L PHE 3.7 0.7 - - - -
144L PHE 2.9 1.8 + - - -
145L PHE* 1.3 74.0 - - - +
147L GLY* 1.3 70.2 + - - +
148L VAL 3.6 3.8 + - - -
149L SER* 4.3 5.1 + - - -
150L GLY* 3.1 10.1 + - - -
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Residues in contact with GLY 147 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L GLY* 3.4 8.0 + - - -
61L GLY* 4.5 1.3 - - - -
92L VAL* 3.2 32.1 - - - -
143L PHE* 2.6 23.3 + - - -
146L GLY* 1.3 77.3 - - - +
148L VAL* 1.3 63.7 + - - -
149L SER 3.1 0.9 + - - -
150L GLY* 2.9 9.5 + - - -
151L VAL* 3.2 12.2 + - - +
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Residues in contact with VAL 148 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89L ALA* 4.5 16.6 - - + +
92L VAL* 3.5 23.6 - - + +
93L VAL* 3.8 7.4 - - + -
144L PHE* 2.9 60.8 + - + +
145L PHE* 3.7 5.5 - - - -
146L GLY 3.6 1.6 + - - -
147L GLY* 1.3 66.9 - - - -
149L SER* 1.3 69.5 + - - +
151L VAL* 4.9 4.5 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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