Contacts of the strand formed by residues 33 - 38 (chain M) in PDB entry 3WIH
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 LEU 33 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4M MET* 3.6 27.8 - - + -
23M CYS* 3.7 9.4 - - - -
29M ILE* 3.7 6.1 - - + -
31M ASN 2.8 8.9 + - - -
32M PHE* 1.3 74.1 - - - +
34M ASN* 1.3 66.6 + - - +
35M TRP* 3.2 37.2 - - + +
48M ILE 4.4 0.3 - - - +
49M TYR 3.9 0.5 - - - -
50M TYR* 3.3 4.5 + - - +
51M THR* 2.7 34.4 + - - +
71M PHE* 3.5 56.8 - - + -
88M CYS* 4.3 2.5 - - + -
89M GLN 3.3 6.5 - - - +
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Residues in contact with ASN 34 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103I VAL 5.4 1.6 + - - -
104I TYR 4.7 2.0 - - - -
105I PRO* 3.7 26.8 - - - +
32M PHE 5.4 0.8 - - - -
33M LEU* 1.3 76.4 + - - +
35M TRP* 1.3 64.5 + - - +
36M TYR* 3.9 13.2 - - + +
46M LEU* 4.2 1.8 - - + -
48M ILE 3.2 9.0 - - - +
49M TYR* 3.3 6.8 - - - +
50M TYR* 3.1 31.7 + - - -
87M PHE 3.8 0.2 - - - +
88M CYS* 3.2 6.4 - - - +
89M GLN* 2.8 66.3 + - - +
91M GLY* 5.2 4.8 - - - +
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Residues in contact with TRP 35 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6M GLN* 4.1 7.4 - - - -
21M ILE* 3.6 35.9 - - + -
22M SER 4.2 0.7 - - - -
23M CYS* 3.5 32.8 - - + -
33M LEU* 3.2 24.8 - - + +
34M ASN* 1.3 73.9 - - - +
36M TYR* 1.3 61.8 + - - +
46M LEU* 3.7 4.3 - - - +
47M LEU* 2.9 28.1 + - + -
48M ILE* 2.7 42.9 + - + +
51M THR 4.6 4.6 + - - -
64M GLY* 5.4 0.2 - - - -
65M SER 5.7 0.2 + - - -
72M SER* 3.8 18.0 + - - -
73M LEU* 3.6 48.9 - - + -
86M TYR* 4.5 5.8 - - + -
87M PHE 3.3 19.1 - - - -
88M CYS* 3.9 13.5 - - + -
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Residues in contact with TYR 36 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45I LEU* 6.0 1.3 - - + -
105I PRO* 3.7 5.5 - - - +
106I PHE* 2.9 49.1 + + - -
109I TRP* 3.7 20.4 - + + -
34M ASN* 3.7 8.8 + - + -
35M TRP* 1.3 74.2 - - - +
37M GLN* 1.3 60.4 + - - +
38M GLN 4.2 0.2 - - - -
44M VAL* 4.2 12.3 - - + -
45M LYS 3.3 4.9 - - - +
46M LEU* 3.6 30.5 - - + -
47M LEU* 5.0 1.6 - - - -
85M THR 3.8 0.2 - - - +
86M TYR* 3.3 10.0 - - - +
87M PHE* 2.8 47.6 + - + +
89M GLN* 2.8 45.5 + - + -
98M PHE* 4.1 14.8 - + - -
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Residues in contact with GLN 37 (chain M).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36M TYR* 1.3 74.1 - - - +
38M GLN* 1.3 63.5 - - - +
39M LYS* 3.8 20.3 + - - +
43M THR 3.5 1.9 - - - +
44M VAL* 3.4 4.5 - - - -
45M LYS* 2.9 41.4 + - + +
47M LEU* 3.7 31.5 - - + +
62M PHE* 4.3 11.7 - - - -
81M GLU 4.2 12.3 + - - -
82M ASP* 4.3 1.2 + - - +
84M ALA* 3.7 17.9 - - + +
85M THR 3.6 2.2 - - - -
86M TYR* 3.0 35.4 + - + -
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Residues in contact with GLN 38 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39I LEU* 3.2 30.2 - - - +
95I TYR* 3.4 14.3 + - - -
1001I GOL 4.4 4.6 + - - -
36M TYR 4.2 0.2 - - - -
37M GLN* 1.3 73.6 - - - +
39M LYS* 1.3 71.6 + - - +
42M GLY* 4.0 9.5 - - - +
43M THR 3.3 9.6 - - - +
44M VAL* 4.0 16.2 - - + -
84M ALA* 3.2 6.4 - - - +
85M THR* 2.8 50.6 + - - +
87M PHE* 3.7 26.9 - - + -
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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