Contacts of the strand formed by residues 96 - 102 (chain H) in PDB entry 2P5V
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 VAL 96 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147G LYS* 2.6 35.8 + - + +
149G THR* 4.6 0.7 - - - +
72H ILE* 5.6 0.2 - - + -
90H VAL* 3.8 23.6 - - + +
93H TRP* 3.0 24.5 + - + +
94H PRO 4.2 2.4 - - - +
95H GLU* 1.3 80.1 - - + +
97H LEU* 1.3 58.4 + - - +
98H SER 3.6 24.9 - - - +
110H LEU* 4.1 17.3 - - + -
111H GLN 3.6 6.1 - - - +
112H ALA* 4.2 9.6 - - + -
123H PHE* 4.0 27.1 - - + -
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Residues in contact with LEU 97 (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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147G LYS* 3.6 5.9 - - - +
148G HIS* 3.4 2.8 - - - -
149G THR* 2.9 54.7 + - + +
150G THR* 3.7 22.2 - - - +
151G SER 3.4 22.0 - - - +
152G LEU* 4.1 12.6 - - + -
153G PRO* 4.1 8.7 - - + -
94H PRO 4.0 12.6 - - - +
95H GLU 4.0 7.6 - - - +
96H VAL* 1.3 76.8 - - - +
98H SER* 1.3 62.8 + - - +
111H GLN* 2.9 14.0 + - + +
113H PHE* 4.1 25.1 - - + -
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Residues in contact with SER 98 (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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111G GLN* 5.7 0.2 + - - -
147G LYS* 3.3 6.3 - - - -
148G HIS* 3.2 25.1 - - - -
149G THR 4.4 1.2 + - - -
96H VAL* 3.6 7.0 - - - +
97H LEU* 1.3 82.6 - - - +
99H CYS* 1.3 62.0 + - - +
100H PHE* 3.6 21.9 - - - -
109H LEU 4.3 0.9 - - - -
110H LEU* 3.2 4.2 - - - -
111H GLN* 2.9 49.4 + - - -
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Residues in contact with CYS 99 (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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146G ILE* 2.9 46.2 + - + -
147G LYS* 2.9 15.3 + - + +
86H PHE* 4.1 6.5 - - - -
90H VAL* 3.7 26.9 - - + -
98H SER* 1.3 76.0 - - - +
100H PHE* 1.3 66.1 - - - +
108H TYR* 3.9 17.0 - - - -
109H LEU 3.3 4.3 - - - -
110H LEU* 3.8 27.1 - - + -
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Residues in contact with PHE 100 (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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69G GLN* 3.6 27.8 - - - -
71G PHE* 3.4 30.3 - + - -
111G GLN* 4.0 7.0 - - - -
142G VAL* 3.6 22.9 - - + -
144G LYS 3.5 4.3 - - - +
145G GLU* 3.9 27.4 - - + -
147G LYS 4.4 2.0 - - - -
148G HIS* 4.3 13.9 - + - -
98H SER* 3.6 28.3 - - - -
99H CYS* 1.3 78.6 - - - +
101H ALA* 1.3 61.5 + - - +
102H LEU* 3.5 20.3 + - + +
108H TYR* 3.1 7.7 - - - -
109H LEU* 2.9 42.8 + - + +
111H GLN* 5.1 1.1 - - - -
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Residues in contact with ALA 101 (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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125B LEU* 5.1 2.7 - - + -
142G VAL* 3.6 4.5 - - - -
143G LEU* 2.8 38.3 + - + -
144G LYS* 2.9 30.1 + - + +
146G ILE* 4.3 2.6 - - + +
83H ARG* 4.2 13.7 - - - +
100H PHE* 1.3 70.3 - - - +
102H LEU* 1.3 54.8 + - - +
107H ASP 3.2 10.1 - - - +
108H TYR* 3.7 23.8 - - + +
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Residues in contact with LEU 102 (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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71G PHE* 3.6 33.7 - - + -
140G SER* 4.2 17.9 - - - +
141G PHE 3.4 20.2 - - - +
142G VAL* 4.0 2.0 - - - -
143G LEU* 3.3 15.6 - - - +
73H ARG* 4.7 9.2 - - - +
100H PHE* 3.9 20.0 - - + +
101H ALA* 1.3 74.2 - - - +
103H THR* 1.3 63.8 + - - +
104H GLY 3.4 3.3 + - - +
106H THR* 3.6 24.6 - - - +
107H ASP* 3.0 10.4 + - - +
109H LEU* 3.7 32.8 - - + +
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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