Contacts of the strand formed by residues 100 - 108 (chain A) in PDB entry 2WEA
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 GLN 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.9 14.0 - - + +
87A THR* 3.1 2.2 - - - -
88A ASP 2.9 32.5 + - - +
90A VAL* 3.6 26.7 - - + -
97A ALA* 3.9 15.3 - - + +
98A HIS 3.2 2.5 - - - -
99A GLY* 1.3 77.2 - - - +
101A ALA* 1.3 85.5 + - - +
102A VAL* 3.4 3.5 + - - +
138A THR 2.9 21.4 + - - -
139A THR* 3.8 1.4 - - - +
140A PHE* 3.3 23.0 - - - +
143A THR* 2.7 34.6 + - - -
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Residues in contact with ALA 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LEU* 4.0 10.9 - - - +
85A VAL* 4.1 11.2 - - + -
86A PHE 3.6 4.9 - - - -
87A THR* 4.1 6.7 - - + -
99A GLY 3.6 3.2 + - - -
100A GLN* 1.3 94.5 + - - +
102A VAL* 1.3 60.1 + - - +
103A GLN* 4.2 6.6 + - + +
137A GLN* 3.5 46.7 - - + +
138A THR 4.9 1.5 + - - +
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ILE* 3.9 17.3 - - + -
39A LEU* 4.0 7.4 - - + -
41A VAL* 3.7 33.7 - - + -
57A TYR* 3.8 20.4 - - + -
85A VAL* 3.5 2.2 - - - -
86A PHE* 2.7 38.0 + - - +
88A ASP* 4.2 8.1 - - + -
90A VAL* 3.8 24.5 - - + -
100A GLN 3.6 11.0 - - - +
101A ALA* 1.3 77.6 - - - +
103A GLN* 1.3 60.8 + - - +
104A ALA 3.4 4.5 + - - -
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Residues in contact with GLN 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 2.4 32.3 + - - +
39A LEU* 2.9 31.1 + - - +
40A TRP* 3.1 6.8 - - + +
41A VAL* 2.9 27.9 + - - -
71A TRP* 3.3 39.7 - - + +
84A ASN 3.5 6.5 - - - -
85A VAL* 4.5 4.9 - - + +
101A ALA* 5.0 5.1 - - + +
102A VAL* 1.3 70.7 - - - +
104A ALA* 1.3 63.2 + - - +
130A ASN* 3.1 23.6 + - - -
132A VAL* 3.5 21.2 - - + +
137A GLN* 5.6 0.5 - - - +
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.9 8.7 - - - -
43A SER* 3.9 14.1 - - - +
45A GLU* 3.5 19.7 - - - +
57A TYR* 4.4 9.4 - - + -
59A PRO* 5.1 0.7 - - + -
71A TRP* 3.2 4.4 + - - -
83A GLY* 3.3 0.3 - - - -
84A ASN* 2.9 36.2 + - - +
86A PHE* 4.1 16.4 - - + -
102A VAL 3.4 2.6 + - - -
103A GLN* 1.3 73.1 - - - +
105A ALA* 1.3 64.0 + - - +
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Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.1 12.6 - - + -
41A VAL 2.8 23.2 + - - +
42A PHE* 4.4 2.2 - - - -
43A SER* 2.8 23.6 + - - -
45A GLU* 3.9 1.4 - - - +
46A LEU* 3.5 19.2 + - + +
71A TRP* 3.7 5.6 - - + -
82A SER 3.6 6.3 - - - +
103A GLN 3.5 1.0 + - - -
104A ALA* 1.3 71.9 - - - +
106A GLN* 1.3 60.5 + - - +
107A GLN 4.5 0.2 - - - +
108A ILE* 3.9 27.8 - - + -
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Residues in contact with GLN 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.5 41.2 + - + +
46A LEU* 3.5 12.8 - - - +
47A PRO* 4.4 7.6 - - - +
82A SER* 2.8 8.8 + - - +
83A GLY* 3.4 21.8 - - - +
84A ASN* 3.5 24.5 + - - +
104A ALA 3.5 0.2 + - - -
105A ALA* 1.3 73.0 - - - +
107A GLN* 1.3 61.6 + - + +
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Residues in contact with GLN 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 4.2 1.6 - - - -
50A GLN* 5.5 0.7 - - - -
80A SER* 3.0 38.4 + - - -
81A ALA* 3.2 7.3 + - - +
82A SER* 2.6 68.9 + - - +
105A ALA* 4.5 0.3 - - - +
106A GLN* 1.3 80.3 - - + +
108A ILE* 1.3 70.9 + - - +
109A SER* 3.6 12.9 - - - +
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Residues in contact with ILE 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TRP* 4.0 20.9 - - + -
42A PHE* 3.5 33.9 - - + -
46A LEU* 4.1 9.4 - - + -
50A GLN* 3.4 24.3 + - + +
80A SER 3.7 4.9 - - - -
81A ALA* 4.0 6.3 - - + -
105A ALA* 3.9 22.0 - - + -
107A GLN* 1.3 87.0 + - - +
109A SER* 1.3 59.9 + - - +
112A PHE* 4.2 7.2 - - + -
113A GLN* 3.1 40.0 + - + +
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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