Contacts of the strand formed by residues 91 - 96 (chain H) in PDB entry 2FIE
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 THR 91 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33H LEU* 3.2 31.2 - - + -
85H LEU* 3.2 24.6 + - + -
86H LYS* 3.7 9.0 + - - -
88H SER* 4.0 3.1 - - - +
89H PHE 3.6 0.2 - - - -
90H ALA* 1.3 75.2 + - - +
92H CYS* 1.3 56.9 + - - +
94H LEU* 3.7 29.4 - - + -
105H VAL* 3.7 10.6 - - - +
109H LYS 3.6 2.6 + - - +
110H ARG* 3.2 8.5 - - - -
111H GLY* 2.7 24.0 + - - +
113H TYR 3.3 5.8 - - - +
115H VAL* 3.9 9.4 - - + -
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Residues in contact with CYS 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H THR* 1.3 75.3 - - - +
93H VAL* 1.3 79.5 + - + +
104H ILE* 3.8 5.7 - - - +
105H VAL* 3.1 30.5 + - - +
110H ARG* 4.2 12.8 - - + -
111H GLY 3.4 18.2 - - - +
113H TYR 3.0 18.4 + - - -
114H VAL* 4.3 2.7 - - - -
141H LYS* 3.5 40.2 - - + -
147H PRO* 4.1 8.8 - - + +
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Residues in contact with VAL 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H CYS* 1.3 96.1 - - - +
94H LEU* 1.3 67.2 - - - +
102H ALA* 4.2 14.4 - - + -
103H ILE 3.6 3.6 - - - -
104H ILE* 3.8 15.7 - - + -
105H VAL* 4.4 0.4 - - - +
113H TYR 3.9 0.2 + - - -
114H VAL* 3.0 25.7 - - + +
115H VAL 3.0 23.0 + - - -
147H PRO* 3.6 20.2 - - + -
148H SER 3.5 26.2 - - - +
151H ASP* 4.4 6.1 - - + -
152H ALA* 4.6 8.3 - - + -
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Residues in contact with LEU 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82H MET* 3.1 41.3 - - + +
85H LEU* 3.5 27.8 - - + -
86H LYS* 4.1 28.9 - - + -
91H THR* 3.7 26.5 - - + -
93H VAL* 1.3 76.1 - - - +
95H VAL* 1.3 62.9 + - - +
102H ALA* 3.6 2.3 - - - -
103H ILE* 2.8 44.1 + - + +
105H VAL* 4.1 12.6 - - + -
115H VAL* 3.3 16.6 - - + +
117H PHE* 4.4 1.3 - - + -
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Residues in contact with VAL 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93H VAL* 4.7 1.8 - - + -
94H LEU* 1.3 79.5 - - - +
96H SER* 1.3 64.5 + - - +
99H ASP 5.8 0.4 - - - +
101H HIS 5.6 0.4 - - - -
102H ALA* 3.7 22.4 - - + +
114H VAL* 5.4 0.4 - - + -
115H VAL 2.8 9.1 + - - +
116H CYS* 4.3 13.0 - - - -
117H PHE* 2.9 33.1 + - - -
152H ALA* 3.8 27.1 - - + -
278H LEU* 5.2 1.3 - - + -
279H TYR* 4.1 24.5 - - + -
310H ILE* 4.1 28.5 - - + +
311H HIS* 4.5 2.9 - - + -
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Residues in contact with SER 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78H ASN* 2.8 27.9 + - - -
82H MET* 4.7 2.2 - - - -
95H VAL* 1.3 78.5 - - - +
97H GLU* 1.3 57.0 + - - +
98H GLU* 2.7 28.4 + - - +
99H ASP* 2.9 37.6 + - - +
101H HIS 5.7 0.4 + - - -
103H ILE* 5.3 0.6 - - - +
117H PHE* 3.1 20.6 - - - -
119H PRO* 3.7 2.6 - - - +
279H TYR* 4.1 4.9 - - - -
311H HIS* 3.6 4.7 - - - -
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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