Contacts of the strand formed by residues 62 - 67 (chain B) in PDB entry 3WTW
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 THR 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A THR* 4.4 15.7 - - + +
149A THR* 4.2 7.2 - - - +
161A THR* 4.4 8.5 - - + -
163A HIS* 4.8 1.9 + - - -
17B PHE* 4.0 30.8 - - + -
21B LEU* 4.8 2.2 - - + -
56B ALA* 3.3 2.3 - - - -
57B PHE* 3.2 30.7 + - + -
60B THR* 3.1 27.8 + - - +
61B GLY* 1.3 75.7 - - - +
63B ASN* 1.3 72.8 + - - +
64B LEU* 4.8 8.6 - - + +
103B LEU* 6.2 0.4 - - + -
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Residues in contact with ASN 63 (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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106A MET* 3.7 32.0 - - + +
107A ALA 3.6 16.3 + - - +
113A TYR 2.5 26.2 + - - -
114A SER* 2.4 31.0 + - - -
147A THR 5.4 0.6 + - - -
149A THR* 3.0 29.8 + - - +
30B THR* 4.0 4.7 + - - +
55B ILE 4.5 0.2 - - - +
56B ALA* 3.3 13.8 - - + +
61B GLY 3.1 10.1 + - - -
62B THR* 1.3 74.5 - - - +
64B LEU* 1.3 70.1 + - - +
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Residues in contact with LEU 64 (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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106A MET* 3.7 9.2 - - - +
149A THR* 4.1 0.9 - - + -
159A VAL* 3.4 43.3 - - + -
161A THR* 6.4 0.2 - - + -
21B LEU* 6.3 0.2 - - + -
54B GLU* 3.7 1.9 - - - -
55B ILE 2.7 40.4 + - - +
57B PHE* 4.3 24.0 - - + -
62B THR* 4.8 7.6 - - + +
63B ASN* 1.3 83.7 - - - +
65B SER* 1.3 68.4 + - - +
66B LEU* 3.7 12.7 + - + +
101B MET* 4.1 22.9 - - + -
103B LEU* 4.3 16.4 - - + -
110B TRP* 4.8 10.3 - - + +
125B LEU* 4.8 2.5 - - + -
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Residues in contact with SER 65 (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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104A THR* 4.7 2.4 - - - +
106A MET* 3.4 21.7 - - - +
151A THR* 3.8 15.0 + - - +
153A PHE* 3.1 36.5 - - - -
157A PRO* 5.2 3.3 - - - +
159A VAL* 5.8 0.3 - - - +
53B SER 3.9 5.2 + - - -
54B GLU* 4.7 9.8 + - - +
64B LEU* 1.3 76.8 - - - +
66B LEU* 1.3 61.1 + - - +
67B GLN 4.3 0.3 + - - -
101B MET* 3.5 20.1 - - - +
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Residues in contact with LEU 66 (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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153A PHE* 5.7 2.8 - - - -
52B ARG* 3.4 6.6 - - - +
53B SER 2.8 38.4 + - - +
55B ILE* 3.5 41.3 - - + +
64B LEU* 4.1 12.8 - - + +
65B SER* 1.3 79.0 + - - +
67B GLN* 1.3 62.1 + - - +
68B PHE* 3.8 17.7 - - + -
99B ALA* 4.3 4.0 - - + -
101B MET* 4.0 18.2 - - + -
110B TRP* 3.5 54.7 - - + -
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Residues in contact with GLN 67 (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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153A PHE* 3.5 35.5 - - + +
154A THR 4.2 6.7 + - - +
155A ASN* 4.3 9.2 - - - +
157A PRO* 3.6 34.7 - - + +
51B GLY 3.5 8.5 - - - +
52B ARG* 5.0 5.8 - - + -
65B SER 4.3 0.6 + - - -
66B LEU* 1.3 74.8 - - - +
68B PHE* 1.3 59.9 + - - +
69B PHE* 3.2 26.0 + - + +
99B ALA* 3.0 20.0 - - - +
100B PRO* 4.1 7.1 - - - +
101B MET* 5.3 0.6 - - - +
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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