Contacts of the strand formed by residues 92 - 105 (chain C) in PDB entry 2BBV
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 92 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C PHE* 3.4 28.3 - - + -
90C GLY 3.6 1.8 - - - +
91C LYS* 1.3 83.0 - - - +
93C VAL* 1.3 62.2 + - - +
94C THR* 4.3 1.3 - - + -
252C PHE* 4.4 2.7 - - + -
320C GLU* 3.7 34.1 - - + +
321C TYR 2.9 15.3 - - - +
322C ARG* 4.2 2.9 - - - -
323C PRO* 3.8 2.5 - - - -
333C GLY* 3.3 1.9 - - - -
334C HIS* 2.9 55.8 + - + +
336C SER* 3.8 13.7 - - - +
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Residues in contact with VAL 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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92C VAL* 1.3 72.5 - - - +
94C THR* 1.3 62.2 + - - +
95C ARG* 3.1 20.5 + - + +
321C TYR* 3.1 32.9 + - + +
323C PRO* 3.3 35.9 - - + -
329C LEU* 4.0 36.1 - - + +
332C PHE* 4.6 9.4 - - + +
333C GLY* 4.4 11.0 - - - +
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Residues in contact with THR 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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81C GLY 4.8 0.2 + - - -
82C LYS* 2.6 37.1 + - - +
83C GLY* 3.9 2.0 - - - -
92C VAL* 4.3 0.7 - - + -
93C VAL* 1.3 71.2 - - - +
95C ARG* 1.3 63.5 - - - +
96C LYS* 3.4 24.8 + - - +
318C CYS* 5.0 5.6 - - - -
319C LEU 3.2 9.2 - - - +
320C GLU* 3.8 23.6 - - + -
334C HIS* 3.0 23.8 + - + +
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Residues in contact with ARG 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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93C VAL* 3.1 11.6 + - + -
94C THR* 1.3 72.7 - - - +
96C LYS* 1.3 75.4 + - - +
97C ASP* 3.1 35.7 + - - +
146C PRO 3.5 20.6 + - - -
147C GLY* 4.3 14.8 + - - -
150C SER* 6.1 0.2 - - - -
151C MET* 4.2 22.7 - - + -
317C ALA 3.9 1.1 - - - +
318C CYS* 3.5 7.1 - - - -
319C LEU* 2.9 33.5 + - + +
321C TYR* 3.6 33.0 - - + -
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Residues in contact with LYS 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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69C CYS* 5.4 0.4 - - - -
79C ASP* 3.7 37.2 + - + +
81C GLY* 2.3 51.8 + - - +
94C THR* 3.4 31.2 + - - +
95C ARG* 1.3 86.0 + - - +
97C ASP* 1.3 61.6 + - - +
98C VAL* 3.5 11.6 - - + +
317C ALA 4.2 2.5 - - - -
318C CYS* 4.1 15.2 - - + +
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Residues in contact with ASP 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95C ARG* 3.1 38.3 + - - +
96C LYS* 1.3 68.2 - - - +
98C VAL* 1.3 65.3 + - - +
120C GLY* 5.0 9.1 + - - -
145C PHE* 3.5 42.5 - - + +
146C PRO* 4.3 1.0 - - - +
316C TRP* 3.3 6.4 - - - +
317C ALA* 3.2 33.8 + - + +
319C LEU* 4.1 18.5 - - - +
321C TYR* 5.2 2.9 + - - -
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Residues in contact with VAL 98 (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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28C GLN* 4.8 3.1 - - - +
79C ASP* 4.8 7.4 - - - +
96C LYS* 3.5 15.5 + - + +
97C ASP* 1.3 79.2 - - - +
99C LEU* 1.3 66.0 - - - +
100C ASN 4.3 0.2 - - - -
145C PHE* 3.5 3.9 - - - -
146C PRO* 3.4 22.1 - - - +
314C LYS* 5.2 8.1 - - + +
315C THR 3.2 3.6 - - - +
316C TRP* 2.9 44.4 - - + +
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Residues in contact with LEU 99 (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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98C VAL* 1.3 75.5 - - - +
100C ASN* 1.3 59.7 + - - +
101C GLN* 3.7 23.6 - - + +
122C ALA* 3.7 9.6 - - + -
123C TYR* 3.7 23.1 - - + -
143C VAL* 4.4 7.4 - - + -
144C ASN 3.0 31.4 - - - +
145C PHE* 3.7 18.8 - - + -
146C PRO* 4.3 7.9 - - + -
313C LEU* 4.3 1.3 - - + -
314C LYS* 2.8 40.2 - - - +
315C THR* 2.9 30.5 + - + -
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Residues in contact with ASN 100 (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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25C VAL* 5.9 0.2 - - - +
98C VAL 4.4 0.2 + - - -
99C LEU* 1.3 75.6 - - - +
101C GLN* 1.3 66.9 + - - +
102C SER* 4.2 1.2 + - - -
146C PRO* 6.1 0.2 - - - +
312C ILE* 3.2 22.2 - - - +
313C LEU 3.5 2.0 - - - -
314C LYS* 2.4 41.2 - - - +
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Residues in contact with GLN 101 (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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99C LEU* 3.7 25.5 - - + +
100C ASN* 1.3 80.7 + - - +
102C SER* 1.3 82.0 + - - +
103C ILE* 4.6 2.9 - - + -
123C TYR* 3.5 26.5 + - + +
143C VAL* 4.2 18.6 - - - +
312C ILE* 3.5 2.4 - - - -
313C LEU* 2.6 48.7 + - + +
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Residues in contact with SER 102 (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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100C ASN* 4.2 3.0 + - - -
101C GLN* 1.3 92.4 + - - +
103C ILE* 1.3 61.0 - - - +
104C ASN* 5.4 2.5 - - - -
311C ALA 3.9 5.2 - - - -
312C ILE* 4.8 9.7 - - - +
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Residues in contact with ILE 103 (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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101C GLN* 4.1 4.7 - - + +
102C SER* 1.3 78.0 - - - +
104C ASN* 1.3 69.9 + - - +
105C PHE* 3.6 39.3 + - + -
111C THR* 5.4 0.7 - - + -
113C ILE* 3.7 19.3 - - + -
123C TYR* 4.0 15.0 - - + +
125C VAL* 5.3 5.8 - - + -
175C ILE* 5.8 0.4 - - + -
310C SER* 3.3 2.8 - - - -
311C ALA* 3.0 49.4 + - + +
313C LEU* 3.8 29.6 - - + -
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Residues in contact with ASN 104 (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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102C SER* 5.4 1.8 - - - -
103C ILE* 1.3 80.4 + - - +
105C PHE* 1.3 64.3 + - - +
106C THR* 3.6 9.3 + - + +
111C THR* 6.0 0.5 - - - +
309C ASN 3.7 6.5 - - - +
310C SER* 3.5 19.4 - - - -
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Residues in contact with PHE 105 (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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103C ILE* 3.6 40.2 - - + -
104C ASN* 1.3 73.5 - - - +
106C THR* 1.3 64.7 + - - +
107C ALA 3.5 2.3 + - - -
111C THR* 3.7 23.3 - - + +
113C ILE* 3.8 13.0 - - + -
175C ILE* 4.7 8.5 - - + -
235C PHE* 3.8 32.3 - + - -
301C VAL* 3.4 43.5 - - + -
303C ALA* 4.5 6.0 - - + +
307C ALA 5.3 1.7 - - - +
309C ASN* 2.7 39.4 + - + +
311C ALA* 4.1 16.6 - - + -
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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