Contacts of the strand formed by residues 71 - 76 (chain B) in PDB entry 1H3F
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 LYS 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B PRO* 4.6 8.9 - - + +
38B LEU 2.9 16.0 + - - +
39B THR* 3.5 9.8 - - - +
40B VAL* 2.8 28.7 + - - -
70B HIS* 1.3 73.1 - - - +
72B VAL* 1.3 69.6 + - - +
73B VAL* 3.9 7.4 + - + -
120B PRO 3.7 15.6 + - - +
121B HIS* 3.7 20.4 - - - +
122B LEU* 3.7 8.1 - - - +
123B PHE 4.5 0.2 - - - -
124B GLU* 2.8 44.8 + - - -
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Residues in contact with VAL 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B VAL* 3.4 12.8 - - + +
62B MET* 3.3 48.7 - - + +
65B PHE* 5.3 1.1 - - + -
66B GLN* 3.5 33.9 - - + +
70B HIS 5.1 0.4 - - - +
71B LYS* 1.3 74.4 - - - +
73B VAL* 1.3 71.8 + - - +
74B LEU* 4.2 2.0 - - + +
116B LEU* 4.4 3.4 - - + -
122B LEU 2.8 12.7 + - - +
123B PHE* 3.3 19.3 - - + -
124B GLU 2.9 25.8 + - - -
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Residues in contact with VAL 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.6 25.6 - - + -
40B VAL 3.0 8.4 + - - +
41B LYS* 3.6 2.6 - - - -
42B LEU 3.2 23.6 + - - +
71B LYS* 4.6 9.6 - - + +
72B VAL* 1.3 79.1 - - - +
74B LEU* 1.3 59.9 + - - +
75B ILE* 3.8 7.7 + - + +
124B GLU* 3.4 23.6 - - + +
126B ARG* 4.0 20.4 - - + +
186B ILE* 3.6 38.6 - - + -
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Residues in contact with LEU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.5 28.9 - - + +
44B ALA* 4.3 6.5 - - + -
62B MET* 5.2 2.0 - - + -
72B VAL* 3.9 5.0 - - + +
73B VAL* 1.3 71.8 - - - +
75B ILE* 1.3 61.4 + - - +
76B ILE* 4.6 4.7 - - + -
108B TYR* 3.4 47.1 - - + +
109B VAL* 4.5 4.9 - - + -
112B ALA* 4.7 8.3 - - + -
116B LEU* 5.0 3.4 - - + -
123B PHE* 3.8 35.9 - - + -
124B GLU 2.9 6.4 + - - +
125B LEU* 3.6 16.9 - - + +
126B ARG* 2.9 26.7 + - - +
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Residues in contact with ILE 75 (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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41B LYS* 4.0 11.4 - - + -
42B LEU 2.8 15.8 + - - +
43B GLY* 3.3 5.9 - - - -
44B ALA 2.8 27.7 + - - -
73B VAL* 4.1 15.0 - - + +
74B LEU* 1.3 78.5 - - - +
76B ILE* 1.3 67.7 + - - +
77B GLY* 3.4 0.7 + - - -
126B ARG* 3.4 5.2 - - + +
128B ASN* 3.8 33.7 - - + +
131B TRP* 4.1 9.4 - - + -
182B ASP* 4.0 22.0 - - + +
186B ILE* 3.8 33.9 - - + -
1433B TYE 4.2 8.1 - - + +
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Residues in contact with ILE 76 (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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44B ALA* 3.7 10.5 - - + +
46B PRO* 3.9 28.3 - - + -
74B LEU* 4.6 2.7 - - + -
75B ILE* 1.3 73.4 - - - +
77B GLY* 1.3 62.3 + - - +
78B ASP* 2.9 13.9 + - + +
101B THR* 5.1 1.1 - - + -
105B ALA* 4.4 18.2 - - + -
108B TYR* 4.5 22.7 - - + -
109B VAL* 4.8 1.1 - - + -
125B LEU* 3.7 29.4 - - + -
126B ARG 2.8 12.2 + - - +
127B TYR* 3.5 33.8 - - + -
128B ASN* 3.1 21.8 + - - -
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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