Contacts of the strand formed by residues 144 - 151 (chain I) in PDB entry 2WW9
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 144 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22I LEU 2.8 29.7 + - - +
24I VAL 3.0 12.8 + - - -
25I SER 3.9 5.4 - - - -
26I PHE* 3.3 24.1 - - - -
90I PHE* 3.4 18.2 - - - -
119I VAL* 3.4 18.1 - - - +
120I ASN 3.2 11.9 + - - -
121I GLN* 4.5 0.5 - - - -
122I ALA* 3.7 12.1 - - - +
143I PRO* 1.4 76.5 + - - +
145I HIS* 1.3 59.1 + - - +
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Residues in contact with HIS 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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546E G 5.2 0.2 - - - -
18I ARG* 3.2 33.7 + - - -
19I GLY 3.2 19.2 + - - -
20I SER* 3.0 25.2 + - - +
21I TYR* 3.5 43.4 + + - +
119I VAL* 3.2 9.0 - - - +
120I ASN* 3.0 51.6 + - + +
122I ALA* 3.8 10.0 - - + +
144I SER* 1.3 72.7 - - - +
146I ILE* 1.4 66.6 + - - +
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Residues in contact with ILE 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18I ARG* 3.4 3.3 - - - +
19I GLY* 2.9 37.5 + - - +
29I THR* 3.6 30.7 - - + -
33I ALA* 4.6 3.1 - - + -
90I PHE* 3.4 28.0 - - + -
91I VAL* 5.0 3.1 - - + -
94I LEU* 3.5 33.2 - - + -
117I ILE* 4.1 15.7 - - + -
118I GLN 3.5 15.0 - - - +
119I VAL* 4.2 11.2 - - + -
120I ASN* 3.9 1.3 - - - -
145I HIS* 1.4 76.6 - - - +
147I GLU* 1.4 78.9 + - - +
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Residues in contact with GLU 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2I ALA* 4.3 3.5 - - - +
3I ARG* 2.9 36.9 + - + +
4I TYR 5.1 2.7 - - - +
17I ALA 4.0 5.2 - - - -
18I ARG* 3.0 33.2 + - + +
94I LEU* 4.9 0.4 - - - -
117I ILE* 3.3 9.1 - - - +
118I GLN* 3.0 55.5 + - + +
120I ASN* 3.0 32.3 + - - +
146I ILE* 1.4 82.9 - - - +
148I LEU* 1.4 60.6 + - - +
149I VAL* 5.7 0.9 - - + -
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Residues in contact with LEU 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17I ALA* 2.7 36.8 + - + +
18I ARG* 4.8 0.5 - - - +
36I ILE* 4.5 3.1 - - + -
91I VAL* 6.4 0.7 - - + -
94I LEU* 3.7 31.9 - - + +
95I LEU* 4.1 20.0 - - + -
98I ALA* 3.8 27.8 - - + -
114I VAL* 3.5 33.4 - - + -
116I HIS 3.9 5.4 - - - +
117I ILE* 4.1 13.0 - - + -
147I GLU* 1.4 74.3 - - - +
149I VAL* 1.3 76.1 + - - +
150I VAL* 4.1 11.2 - - + -
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Residues in contact with VAL 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I ARG* 4.6 17.7 - - + -
4I TYR* 3.4 66.0 - - + +
14I SER* 5.1 0.2 - - - +
15I ALA 3.8 5.4 - - - +
16I SER* 3.6 22.9 - - - +
115I SER 3.3 13.7 + - - -
116I HIS* 3.0 27.9 + - + +
117I ILE* 5.5 0.2 - - - -
147I GLU* 6.2 0.2 - - + -
148I LEU* 1.3 84.5 - - - +
150I VAL* 1.4 66.5 + - - +
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Residues in contact with VAL 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I TYR* 4.2 0.2 + - - -
9I THR* 3.8 0.2 + - - -
14I SER* 3.1 22.4 + - - -
15I ALA* 3.2 32.0 + - + +
41I LEU* 4.3 14.6 - - + -
98I ALA* 5.7 5.4 - - + +
102I ALA* 5.5 1.3 - - + -
112I LEU* 3.9 27.6 - - + -
113I TYR 3.9 5.6 - - - +
114I VAL* 4.0 25.6 - - + -
115I SER 4.1 1.8 - - - +
148I LEU* 4.1 13.2 - - + -
149I VAL* 1.4 79.1 - - - +
151I THR* 1.4 66.3 + - - +
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Residues in contact with THR 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I TYR* 2.8 26.5 + - - -
8I SER 4.4 0.5 + - - -
9I THR* 3.1 40.8 + - - +
13I LYS* 3.4 11.0 - - + +
14I SER* 4.7 0.4 - - - +
112I LEU* 3.0 31.1 - - - +
113I TYR 3.4 6.3 + - - +
115I SER* 3.3 5.4 + - - -
150I VAL* 1.4 73.4 - - - +
152I GLU* 1.4 74.5 + - + +
153I LYS* 3.8 16.8 - - - +
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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