Contacts of the strand formed by residues 14 - 22 (chain I) in PDB entry 2WWB
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 14 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4I TYR* 4.8 3.5 - - - -
9I THR* 2.9 31.3 + - - +
10I ASN 3.6 8.7 - - - -
11I PRO* 3.7 21.2 + - - +
13I LYS* 1.4 76.2 - - - +
15I ALA* 1.4 73.7 + - - +
16I SER* 4.3 5.5 + - - -
105I LYS* 5.1 4.2 - - - +
107I LEU* 3.5 15.5 - - - +
150I VAL* 3.1 12.8 + - - -
151I THR* 4.5 0.2 - - - +
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Residues in contact with ALA 15 (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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14I SER* 1.4 79.6 + - - +
16I SER* 1.4 64.9 + - - +
98I ALA 4.3 3.6 - - - +
101I ASN* 4.5 4.9 - - + +
102I ALA* 3.7 39.0 - - + +
105I LYS* 5.5 1.8 - - + -
149I VAL* 3.8 0.9 - - - -
150I VAL* 3.1 41.3 + - + +
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Residues in contact with SER 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546E G 3.9 0.3 + - - -
547E A 3.5 36.9 + - - +
548E G 5.1 2.8 + - - -
3I ARG* 5.0 6.1 + - - +
14I SER* 4.3 4.9 + - - -
15I ALA* 1.4 80.9 + - - +
17I ALA* 1.4 61.0 + - - +
98I ALA* 4.4 4.7 - - - +
101I ASN* 2.9 27.7 + - - +
148I LEU 3.7 7.0 - - - -
149I VAL* 3.6 18.7 - - - +
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Residues in contact with ALA 17 (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 3.5 9.6 - - - -
16I SER* 1.4 76.8 - - - +
18I ARG* 1.4 68.3 + - - +
94I LEU* 3.6 20.2 - - + -
97I ASN* 3.4 17.3 - - - +
98I ALA* 3.8 24.5 - - + +
148I LEU* 2.7 32.9 + - + +
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Residues in contact with ARG 18 (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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545E A 3.7 3.1 + - - -
546E G 2.8 67.2 + - - +
547E A 3.3 23.1 - - - +
2I ALA* 3.5 20.0 - - - +
3I ARG* 4.1 9.6 - - + +
16I SER* 6.1 0.2 - - - -
17I ALA* 1.4 82.2 - - - +
19I GLY* 1.4 58.8 + - - +
94I LEU* 4.0 8.5 - - - +
97I ASN* 4.5 4.5 - - - +
120I ASN* 4.4 1.4 + - - -
145I HIS* 3.0 32.6 + - - -
146I ILE 3.3 12.1 - - - +
147I GLU* 2.8 44.9 + - + +
148I LEU 4.8 0.2 - - - +
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Residues in contact with GLY 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545E A 4.7 2.0 - - - -
18I ARG* 1.4 74.4 - - - +
20I SER* 1.4 62.1 + - - -
22I LEU* 4.5 14.8 - - - -
90I PHE* 4.6 1.3 - - - -
94I LEU* 4.2 5.5 - - - +
145I HIS* 3.4 7.7 - - - -
146I ILE* 2.8 46.2 + - - +
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Residues in contact with SER 20 (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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544E A 5.4 3.8 + - - +
545E A 3.6 38.2 + - - +
546E G 3.6 9.2 + - - -
19I GLY* 1.4 75.3 - - - -
21I TYR* 1.4 79.8 + - - +
22I LEU* 3.3 19.5 + - - +
145I HIS* 2.9 26.9 - - - -
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Residues in contact with TYR 21 (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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545E A 6.5 0.7 - - - -
1662F A 5.4 2.3 + - - -
20I SER* 1.4 90.0 - - - +
22I LEU* 1.4 64.1 + - - +
23I ARG* 4.1 6.9 + - - +
122I ALA* 3.7 43.1 - - + -
123I PRO* 5.4 1.8 - - + -
143I PRO* 6.1 0.2 - - - -
145I HIS* 3.6 29.8 + + - +
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Residues in contact with LEU 22 (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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543E A 6.0 2.9 - - + +
544E A 4.7 27.8 - - + +
19I GLY* 4.5 5.6 - - - -
20I SER 3.6 24.9 - - - +
21I TYR* 1.4 79.7 - - - +
23I ARG* 1.4 59.5 + - - +
24I VAL* 3.1 7.4 + - + +
90I PHE* 3.7 33.7 - - + -
122I ALA* 5.1 0.3 - - - +
143I PRO* 3.7 2.3 - - - +
144I SER 2.8 37.8 + - - +
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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