Contacts of the strand formed by residues 77 - 82 (chain A) in PDB entry 3FH4
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 SER 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A LYS 3.9 0.2 - - - +
67A GLN* 3.2 4.5 - - - -
68A VAL* 2.6 41.8 + - - +
70A HIS* 2.7 29.0 + - - -
76A LYS* 1.3 70.6 - - - +
78A VAL* 1.3 61.0 + - - +
147A ALA 3.3 11.4 - - - -
148A TYR* 3.7 2.9 - - - -
149A ALA* 2.9 19.0 + - - +
157A GLY* 3.9 5.9 - - - -
161A LEU* 4.1 22.9 - - - -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A SER* 3.5 38.8 - - - +
49A ILE* 4.2 4.5 - - + -
50A ALA* 3.9 22.0 - - + +
53A TRP* 3.5 24.2 - - + -
65A VAL* 4.2 6.7 - - + -
66A LYS 3.5 10.1 - - - +
67A GLN* 4.0 6.1 - - + -
77A SER* 1.3 73.2 - - - +
79A VAL* 1.3 65.5 + - - +
98A LEU* 4.0 11.0 - - + -
145A PHE 3.7 0.3 - - - +
146A MET* 3.3 5.0 - - - +
147A ALA* 2.8 47.1 + - + +
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Residues in contact with VAL 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A SER 3.7 1.0 - - - +
65A VAL* 3.5 1.1 - - - -
66A LYS* 2.9 46.3 + - + +
68A VAL* 4.2 17.9 - - + -
78A VAL* 1.3 82.6 - - - +
80A MET* 1.3 63.8 + - - +
81A THR* 3.8 24.6 + - + +
144A ALA* 4.3 1.1 - - + -
145A PHE 3.3 7.6 - - - +
146A MET* 4.1 24.2 - - + -
161A LEU* 3.8 27.6 - - + -
165A TYR* 4.2 6.1 - - + +
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Residues in contact with MET 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP* 3.9 26.2 - - + +
57A SER* 4.0 23.8 - - - -
60A LEU* 3.9 17.9 - - + -
63A ALA* 4.0 2.2 - - + -
64A SER 3.1 12.3 - - - +
65A VAL* 4.0 8.7 - - + +
79A VAL* 1.3 74.1 - - - +
81A THR* 1.3 65.1 - - - +
82A ILE* 3.9 26.9 - - + -
129A ILE* 3.8 40.2 - - + -
144A ALA* 3.3 3.1 - - - +
145A PHE* 2.7 49.1 + - + +
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A ASN 3.8 1.0 + - - +
63A ALA* 3.1 7.4 - - - +
64A SER* 2.8 56.5 + - - +
66A LYS* 5.4 6.0 + - + +
79A VAL* 3.8 20.2 - - + +
80A MET* 1.3 78.4 - - - +
82A ILE* 1.3 63.9 + - - +
83A THR* 4.1 5.3 - - - +
91A TRP* 3.7 35.1 - - + -
143A ILE 3.2 3.1 - - - -
144A ALA* 4.2 3.4 - - + -
165A TYR* 4.8 3.6 - - - +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A LEU* 3.5 26.9 - - + -
61A PRO 4.5 17.3 - - - +
62A ASN* 3.8 4.3 - - + +
63A ALA* 4.2 2.5 - - + -
80A MET* 3.9 14.4 - - + -
81A THR* 1.3 76.4 - - - +
83A THR* 1.3 66.5 + - - +
132A LEU* 5.2 3.8 - - + -
137A PHE* 4.5 20.9 - - + +
139A PRO* 3.7 29.1 - - + +
141A ARG 4.1 1.2 - - - +
142A SER* 3.3 1.3 - - - -
143A ILE* 2.8 38.8 + - + +
145A PHE* 3.7 28.0 - - + -
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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