Contacts of the strand formed by residues 34 - 39 (chain M) in PDB entry 3H3P
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 34 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4M LEU* 4.8 6.7 - - + -
23M CYS* 4.1 20.4 - - - -
29M VAL* 4.9 7.6 - - + -
32M ASN 2.8 8.3 + - - +
33M LYS* 1.3 74.3 - - - +
35M ALA* 1.3 64.5 + - - +
36M TRP* 3.6 29.4 - - + +
49M ILE* 4.5 1.4 - - - +
50M TYR* 3.9 1.0 + - - -
51M GLY 3.6 2.0 + - - -
52M ALA* 2.9 29.3 + - - +
66M SER 5.6 0.2 - - - +
72M PHE* 3.3 64.4 - - + -
89M CYS* 4.6 0.9 - - + -
90M GLN 3.2 11.9 - - - +
91M GLN* 5.1 0.4 - - + -
92M TYR* 3.5 3.6 - - - -
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Residues in contact with ALA 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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113I ALA* 3.7 28.5 - - + -
34M LEU* 1.3 74.0 - - - +
36M TRP* 1.3 65.0 + - - +
37M TYR* 3.8 19.7 - - + +
47M LEU* 4.0 0.9 - - + -
49M ILE 3.3 13.0 - - - +
50M TYR* 4.1 1.6 - - - +
88M TYR 3.8 0.2 - - - +
89M CYS* 3.3 5.7 - - - +
90M GLN* 2.8 37.0 + - - +
92M TYR* 3.7 8.2 - - + -
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Residues in contact with TRP 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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6M GLN* 3.9 17.3 - - - -
21M LEU* 4.1 14.4 - - + -
22M SER 4.0 6.1 - - - -
23M CYS* 3.5 38.1 - - + -
34M LEU* 3.6 19.8 - - + +
35M ALA* 1.3 77.0 - - - +
37M TYR* 1.3 65.4 + - - +
47M LEU* 3.8 1.7 - - - +
48M LEU* 3.0 26.0 + - + -
49M ILE* 2.9 37.4 + - + +
52M ALA 4.8 2.7 + - - -
65M GLY* 5.1 0.4 - - - -
66M SER 5.5 0.2 + - - -
72M PHE* 4.1 4.6 - - + +
73M THR 3.8 17.1 + - - -
74M LEU* 3.6 55.2 - - + -
87M TYR* 4.8 2.2 - - + -
88M TYR 3.3 21.3 - - - -
89M CYS* 3.8 12.1 - - + -
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Residues in contact with TYR 37 (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* 5.3 0.9 - - + -
113I ALA* 3.6 4.7 - - - +
114I PHE* 3.0 50.2 + + - -
117I TRP* 3.8 17.7 - + - -
35M ALA* 3.8 8.3 - - + -
36M TRP* 1.3 75.0 - - - +
38M GLN* 1.3 60.8 + - - +
45M PRO* 4.3 13.2 - - + -
46M ARG 3.3 9.9 - - - +
47M LEU* 3.6 26.9 - - + -
48M LEU* 4.4 4.5 - - - +
87M TYR* 3.2 9.2 - - - +
88M TYR* 2.8 47.8 + - + +
90M GLN* 2.6 42.5 + - + -
99M PHE* 3.8 16.6 - + - -
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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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37M TYR* 1.3 75.4 - - - +
39M GLN* 1.3 63.9 + - - +
40M ARG* 3.5 20.6 + - + +
44M ALA 4.3 0.3 - - - +
45M PRO* 3.2 3.5 - - - +
46M ARG* 2.8 64.8 + - + +
48M LEU* 3.8 16.1 - - + +
63M PHE* 3.8 17.4 - - - -
82M GLU 3.9 15.3 + - - -
83M ASP* 3.9 1.2 + - - +
85M ALA* 3.9 15.3 - - + -
86M VAL 3.5 3.1 - - - -
87M TYR* 2.8 35.7 + - + -
88M TYR* 5.7 0.2 - - - -
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Residues in contact with GLN 39 (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 GLN* 2.9 42.2 + - - -
45I LEU* 4.6 0.4 - - - +
95I TYR* 3.5 7.9 + - - -
38M GLN* 1.3 76.6 - - - +
40M ARG* 1.3 66.5 + - - +
41M PRO* 4.7 0.2 - - - +
42M GLY 5.8 0.6 - - - +
43M GLN 3.0 28.5 + - - +
44M ALA 4.8 1.1 - - - -
45M PRO* 3.8 25.3 - - + +
85M ALA* 3.7 3.4 - - - -
86M VAL* 2.8 40.7 + - + +
88M TYR* 3.3 23.1 + - + -
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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