Contacts of the strand formed by residues 88 - 97 (chain C) in PDB entry 3V5I
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 88 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48C LEU* 4.1 11.7 - - + -
60C ILE* 3.5 15.7 - - + +
62C LEU* 3.9 25.6 - - + -
81C ILE* 3.8 32.6 - - + +
84C ILE* 3.9 26.7 - - + -
86C PRO 3.6 3.1 + - - +
87C ASP* 1.3 76.5 - - - +
89C GLN* 1.3 72.4 + - - +
90C THR* 4.5 3.4 - - + -
107C GLY* 3.3 4.9 - - - -
108C ALA* 2.9 31.9 + - - +
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Residues in contact with GLN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ASP* 3.5 23.8 + - + +
60C ILE 2.7 16.5 + - - +
61C TYR* 3.5 33.5 + - + -
62C LEU* 2.8 30.1 + - - +
88C VAL* 1.3 73.2 - - - +
90C THR* 1.3 61.4 + - - +
91C ILE* 4.2 5.4 - - + +
111C LYS* 3.3 44.6 - - + +
113C PHE* 3.1 25.4 - - + -
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Residues in contact with THR 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62C LEU* 3.3 17.9 - - + -
64C ILE* 4.1 12.8 - - + -
81C ILE* 5.2 2.2 - - + -
88C VAL* 3.7 4.9 + - + +
89C GLN* 1.3 77.2 - - - +
91C ILE* 1.3 60.7 + - - +
103C LEU 3.7 15.3 - - - +
104C LEU* 2.7 31.1 + - - +
107C GLY* 3.7 17.0 - - - -
111C LYS 3.1 5.1 + - - +
112C ARG* 3.4 14.9 - - - +
113C PHE 2.7 32.8 + - - -
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Residues in contact with ILE 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C TYR* 4.3 25.8 - - + -
62C LEU 3.0 8.6 + - - +
63C TYR* 3.3 53.7 - - + +
64C ILE* 2.8 26.2 + - - -
89C GLN* 4.7 6.1 - - + +
90C THR* 1.3 80.2 - - - +
92C CYS* 1.3 62.8 + - - +
93C ILE* 3.6 5.3 + - + -
104C LEU* 4.4 1.3 - - - -
113C PHE* 3.5 24.7 - - + -
115C LEU* 4.4 11.2 - - + -
190C MET* 4.0 24.5 - - + -
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Residues in contact with CYS 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE* 3.4 9.0 - - + +
91C ILE* 1.3 71.5 - - - +
93C ILE* 1.3 64.3 + - - +
95C MET 3.9 3.1 - - - -
96C ALA* 3.5 35.9 - - + -
104C LEU* 3.6 29.1 - - + +
113C PHE 3.0 12.1 + - - +
114C ALA* 4.1 5.4 - - + -
115C LEU* 3.1 26.0 + - - +
118C ALA* 3.4 21.0 - - - +
119C GLU 3.8 6.1 - - - -
120C VAL* 4.6 2.2 - - - -
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Residues in contact with ILE 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ALA 6.3 0.2 - - - -
42B ASN* 4.9 4.9 - - - +
45B VAL* 3.7 37.7 - - + -
76B ALA* 3.9 15.3 - - + +
80B THR* 4.4 5.4 - - - +
31C MET* 4.4 9.4 - - + -
63C TYR* 4.0 29.8 - - + -
64C ILE 3.0 10.4 + - - +
65C ASN* 3.1 28.6 - - + +
91C ILE* 3.6 2.2 + - + -
92C CYS* 1.3 78.8 - - - +
94C GLY* 1.3 61.8 + - - +
95C MET 3.0 8.4 + - - -
115C LEU* 3.8 28.7 - - + -
118C ALA* 4.3 1.1 - - - -
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Residues in contact with GLY 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 3.3 33.7 - - - +
75B PHE* 4.6 3.1 - - - +
76B ALA* 3.6 16.7 - - - +
79B ASP* 5.8 1.4 + - - +
65C ASN* 3.8 2.9 - - - -
93C ILE* 1.3 68.8 - - - +
95C MET* 1.3 62.1 + - - +
117C ASN 4.3 2.1 - - - +
118C ALA* 3.4 11.7 - - - +
119C GLU* 2.9 24.1 + - - +
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Residues in contact with MET 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B THR* 3.8 24.5 - - + +
142B HIS* 4.7 2.9 - - + -
65C ASN* 3.1 13.3 + - - +
66C SER 2.9 31.0 + - - +
67C PRO* 5.2 2.7 - - + -
92C CYS* 3.9 3.4 - - - -
93C ILE 3.0 4.9 + - - -
94C GLY* 1.3 74.7 - - - +
96C ALA* 1.3 64.4 + - - +
97C ALA* 4.1 25.6 - - + +
119C GLU* 3.1 52.5 - - + +
121C MET* 4.3 7.2 - - + -
174C PHE* 3.9 24.2 - - + -
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Residues in contact with ALA 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64C ILE* 4.2 10.8 - - + -
66C SER 3.6 4.7 - - - +
92C CYS* 3.5 19.7 - - - -
95C MET* 1.3 75.2 - - - +
97C ALA* 1.3 58.6 + - - +
100C GLY 4.1 5.6 - - - +
101C SER* 3.3 22.2 - - - +
104C LEU* 4.0 16.4 - - + -
119C GLU 2.9 9.4 + - - +
120C VAL* 3.3 5.1 - - + -
121C MET 3.1 20.0 + - - -
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66C SER 3.0 10.0 + - - +
67C PRO* 3.8 15.9 - - + +
68C GLY* 3.4 8.5 - - - -
95C MET* 4.1 13.7 - - + -
96C ALA* 1.3 73.5 - - - +
98C ALA* 1.3 63.3 + - + +
100C GLY* 2.8 26.7 + - - -
101C SER 3.9 0.4 - - - +
121C MET* 3.4 34.5 - - + +
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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