Contacts of the strand formed by residues 34 - 39 (chain X) in PDB entry 3HI6
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 MET 34 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4X LEU* 3.9 26.0 - - + -
22X CYS* 4.7 2.0 - - - -
27X PHE* 4.5 1.8 - - - -
29X PHE* 3.6 39.5 - - + -
32X TYR* 4.2 6.7 - - - -
33X VAL* 1.3 80.6 - - - +
35X TRP* 1.3 64.1 + - - +
50X TYR* 3.2 4.7 - - - +
51X ILE* 3.0 34.1 + - + +
70X ILE* 3.9 0.3 - - - +
72X ARG* 3.7 19.5 - - - +
79X LEU* 3.7 32.1 - - + -
97X ALA 3.5 20.4 - - - +
98X SER* 3.8 16.6 - - - -
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Residues in contact with TRP 35 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33X VAL* 3.6 6.8 - - + +
34X MET* 1.3 82.0 - - - +
36X TRP* 1.3 64.7 - - - +
37X VAL* 4.1 7.2 - - + -
47X TRP* 3.8 26.2 - + + -
49X SER 3.4 9.9 - - - -
50X TYR* 3.4 46.9 - + + +
79X LEU* 3.7 2.4 - - - +
96X CYS* 3.1 10.9 - - - +
97X ALA 2.7 42.4 + - - +
99X SER* 3.0 35.4 + - - +
104X SER 4.4 3.6 - - - -
105X ASN* 3.5 18.4 - - - -
106X ALA 5.3 0.2 + - - -
107X PHE* 3.5 28.0 - + + -
95Y PRO* 3.4 38.1 - - + -
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Residues in contact with TRP 36 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6X GLU* 3.9 20.6 - - + -
20X LEU* 3.6 37.9 - - + -
21X SER 3.9 6.7 - - - -
22X CYS* 3.8 22.0 - - + -
35X TRP* 1.3 72.9 - - - +
37X VAL* 1.3 64.3 + - - +
47X TRP* 3.7 1.0 - - - +
48X VAL* 3.1 39.7 + - + -
49X SER* 2.9 14.8 + - - +
70X ILE* 3.5 22.7 - - + -
79X LEU* 3.5 35.4 - - + +
80X TYR 3.2 16.6 + - - -
81X LEU* 3.5 34.5 - - + +
94X TYR* 4.4 8.7 - - + -
95X TYR 3.2 21.1 - - - -
96X CYS 4.0 2.9 - - - -
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Residues in contact with VAL 37 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35X TRP* 4.1 7.0 - - + -
36X TRP* 1.3 80.2 - - - +
38X ARG* 1.3 60.9 + - - +
45X LEU* 4.1 17.7 - - + -
46X GLU 3.4 28.0 - - - +
47X TRP* 3.9 6.3 - - + +
48X VAL* 4.5 0.7 - - - +
94X TYR* 3.7 1.5 - - - -
95X TYR* 2.7 44.8 + - - +
97X ALA* 4.7 2.7 - - + -
107X PHE* 3.8 32.1 - - + -
110X TRP* 4.0 27.6 - - + -
97Y PHE* 5.1 4.5 - - + -
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Residues in contact with ARG 38 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37X VAL* 1.3 76.7 - - - +
39X GLN* 1.3 62.7 + - - +
40X ALA 5.3 0.9 - - - +
44X GLY 3.7 0.9 - - - +
45X LEU* 3.6 2.9 - - - -
46X GLU* 2.8 62.2 + - - +
48X VAL* 3.4 22.6 - - + +
63X SER* 3.5 23.2 + - - -
64X VAL* 3.8 13.0 - - - +
68X PHE* 3.9 2.8 - - - -
89X GLU* 4.3 10.1 + - - +
90X ASP* 2.9 34.4 + - - +
92X ALA* 3.9 12.3 - - + -
93X VAL 3.1 10.5 - - - +
94X TYR* 3.1 41.7 + - + -
95X TYR* 5.1 0.2 - - - -
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Residues in contact with GLN 39 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38X ARG* 1.3 74.9 - - - +
40X ALA* 1.3 69.7 + - - +
41X PRO* 3.9 0.3 - - - +
42X GLY 5.7 0.2 - - - +
43X LYS 2.9 29.7 + - - +
44X GLY 3.7 12.4 - - - +
45X LEU* 3.9 18.0 - - + +
92X ALA* 3.4 3.1 - - - -
93X VAL* 2.8 38.5 + - + +
95X TYR* 4.0 10.1 + - + -
38Y GLN* 2.9 41.7 + - - -
87Y TYR* 3.3 13.1 + - - -
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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