Contacts of the strand formed by residues 110 - 120 (chain H) in PDB entry 1CBV
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 TYR 110 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1H GLU* 3.8 32.5 - - - +
2H VAL* 4.6 18.1 - - + +
4H PRO* 4.1 11.2 - - + +
27H PHE* 5.6 5.6 - + - -
98H CYS 3.6 0.9 - - - +
99H VAL* 3.1 5.7 - - - +
100H ARG* 2.8 55.1 + - + +
102H GLN* 3.2 38.1 - - + +
109H ALA* 1.3 79.5 - - + +
111H TRP* 1.3 62.4 + - - +
60L PHE* 3.7 28.3 - + - -
61L SER* 5.4 4.5 + - - -
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Residues in contact with TRP 111 (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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1H GLU* 5.4 2.5 + - - +
4H PRO* 4.2 5.8 - - - +
37H VAL* 3.3 28.0 - - + -
45H LEU* 4.4 8.1 - - + -
97H TYR* 3.9 20.4 - + + -
98H CYS 3.3 4.7 - - - -
99H VAL* 3.3 23.3 - - + -
108H PHE* 3.1 22.3 + + + -
109H ALA 3.4 16.2 - - - -
110H TYR* 1.3 75.6 - - - +
112H GLY* 1.3 68.1 + - - +
41L TYR* 3.3 30.1 - + - -
48L SER* 3.7 11.4 + - - -
49L PRO* 3.7 44.4 + - + +
50L LYS* 4.8 6.1 - - - +
103L PHE* 3.5 37.0 - + - -
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Residues in contact with GLY 112 (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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4H PRO* 3.5 29.6 - - - +
6H GLU* 4.1 8.3 + - - -
97H TYR* 3.0 17.9 - - - -
98H CYS 3.1 13.1 + - - +
111H TRP* 1.3 73.9 - - - +
113H GLN* 1.3 70.3 + - - -
114H GLY* 2.9 6.2 + - - -
48L SER* 3.2 8.6 - - - -
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Residues in contact with GLN 113 (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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1H GLU* 6.2 0.2 - - - +
3H GLN* 4.9 8.3 - - - +
4H PRO* 4.2 7.2 + - - +
5H VAL* 3.9 32.5 - - + +
6H GLU* 4.6 1.7 + - - +
95H MET* 4.5 7.3 - - - +
97H TYR* 3.6 11.7 + - - -
111H TRP 5.3 0.2 - - - +
112H GLY* 1.3 75.0 - - - -
114H GLY* 1.3 61.3 + - - +
47L GLN* 5.2 2.1 - - - -
48L SER* 3.4 18.2 + - - +
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Residues in contact with GLY 114 (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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6H GLU* 3.2 24.8 + - - +
95H MET* 3.9 3.4 - - - -
96H TYR 3.0 17.3 - - - -
97H TYR* 3.5 14.1 - - - -
112H GLY 2.9 3.4 + - - -
113H GLN* 1.3 83.0 - - - +
115H THR* 1.3 66.0 + - - -
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Residues in contact with THR 115 (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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6H GLU* 4.3 18.9 + - + +
7H THR* 4.5 11.7 - - - +
9H GLY* 4.0 28.2 + - - +
20H LEU* 5.1 5.8 - - + -
95H MET* 2.9 25.1 - - - +
96H TYR* 2.6 44.6 + - + +
114H GLY* 1.3 75.9 - - - +
116H LEU* 1.3 65.7 + - - +
117H VAL* 5.2 0.4 - - + -
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Residues in contact with LEU 116 (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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9H GLY* 3.0 11.1 - - - -
10H GLY* 2.9 24.3 + - - +
41H PRO* 5.5 8.7 - - + -
93H THR* 5.6 2.0 - - + -
94H ALA* 3.9 11.4 - - - +
95H MET* 3.9 26.0 - - + +
115H THR* 1.3 81.4 + - - +
117H VAL* 1.3 68.3 + - - +
118H THR* 4.1 17.3 - - + +
156H GLU* 3.2 37.0 - - + +
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Residues in contact with VAL 117 (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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9H GLY* 4.2 2.9 - - - -
10H GLY 3.5 3.1 - - - +
12H VAL* 4.7 2.2 - - + -
18H LEU* 4.0 24.2 - - + -
20H LEU* 3.7 30.7 - - + -
85H MET* 4.1 15.3 - - + -
88H LEU* 4.8 3.1 - - + -
92H ASP 5.0 3.6 - - - +
93H THR* 3.0 21.5 - - - +
94H ALA 3.0 22.9 + - - +
96H TYR* 3.8 18.4 - - + -
115H THR* 5.2 1.1 - - + -
116H LEU* 1.3 81.7 - - - +
118H THR* 1.3 59.9 + - - +
119H VAL* 4.3 17.5 - - + -
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Residues in contact with THR 118 (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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10H GLY 2.6 15.1 + - - +
11H LEU* 3.3 23.4 - - + +
12H VAL* 2.8 32.6 + - - +
93H THR* 3.6 16.8 - - + -
116H LEU* 4.4 15.5 - - + +
117H VAL* 1.3 72.2 + - - +
119H VAL* 1.3 61.1 + - - +
120H SER* 4.1 1.7 + - - -
154H PHE* 4.8 16.8 - - + -
155H PRO* 5.5 1.3 - - + -
156H GLU* 5.0 14.8 + - + +
183H TYR* 5.0 11.7 - - + +
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Residues in contact with VAL 119 (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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12H VAL* 3.3 28.3 - - + +
14H PRO* 3.5 32.3 - - + -
88H LEU* 4.2 13.7 - - + -
89H LYS* 3.2 40.6 - - - +
90H THR* 3.3 11.8 - - - +
93H THR* 2.9 28.7 + - - +
117H VAL* 4.3 13.0 - - + -
118H THR* 1.3 72.2 - - - +
120H SER* 1.3 63.2 + - - +
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Residues in contact with SER 120 (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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12H VAL 3.5 7.5 + - - +
13H GLN* 3.7 6.8 - - - +
14H PRO* 3.4 11.7 - - - +
90H THR* 3.9 11.9 - - - +
118H THR* 4.1 2.6 - - - -
119H VAL* 1.3 79.6 - - - +
121H ALA* 1.3 61.9 + - - +
122H ALA* 3.8 12.0 + - - +
154H PHE* 3.5 38.0 - - - -
181H GLY 5.2 2.4 + - - -
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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