Contacts of the strand formed by residues 97 - 103 (chain E) in PDB entry 3CB4
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 GLY 97 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6E ASN 3.3 4.2 + - - -
7E PHE* 3.2 22.7 - - - -
8E SER 3.4 2.3 + - - -
95E CYS* 3.4 8.3 - - - +
96E GLU* 1.3 81.4 - - - +
98E ALA* 1.3 63.5 + - - +
124E LEU* 4.0 6.7 - - - +
125E GLU 3.1 17.7 - - - -
180E ILE* 3.7 14.2 - - - +
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Residues in contact with ALA 98 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 4.3 2.2 - - - +
8E SER* 3.5 23.1 - - - +
10E ILE* 4.3 20.6 - - + -
92E LEU* 4.9 0.4 - - + -
97E GLY* 1.3 75.4 - - - +
99E LEU* 1.3 63.4 + - - +
100E LEU 3.8 0.4 + - - -
119E ALA* 4.8 3.4 - - + -
124E LEU* 4.7 8.9 - - + +
125E GLU 2.8 7.3 + - - +
126E VAL* 3.2 15.6 - - + +
127E VAL* 2.8 27.1 + - - +
180E ILE* 4.3 1.7 - - - +
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Residues in contact with LEU 99 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E PHE* 3.7 32.8 - - + -
8E SER 3.0 9.8 + - - +
9E ILE* 3.6 14.5 - - + -
10E ILE* 2.8 31.6 + - - +
20E LEU* 3.9 19.7 - - + -
24E ILE* 4.2 5.4 - - + -
98E ALA* 1.3 73.7 - - - +
100E LEU* 1.3 59.2 + - - +
101E VAL* 3.7 9.4 + - + +
126E VAL* 5.3 0.2 - - - -
127E VAL* 3.5 33.9 - - + +
129E VAL* 4.3 4.3 - - + -
172E VAL* 4.2 12.6 - - + -
176E LEU* 3.8 25.4 - - + -
180E ILE* 5.2 0.7 - - + -
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Residues in contact with LEU 100 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ILE* 3.6 28.9 - - + +
98E ALA 3.8 1.8 + - - -
99E LEU* 1.3 69.9 - - - +
101E VAL* 1.3 61.4 + - - +
102E VAL* 3.5 20.8 + - + +
108E VAL* 4.8 3.1 - - + -
112E THR* 4.3 15.7 - - - +
116E CYS* 4.0 27.6 - - + -
126E VAL* 4.1 16.6 - - + +
127E VAL 2.8 14.2 + - - +
128E PRO* 3.8 3.3 - - + +
129E VAL* 3.0 25.4 + - - -
147E ILE* 3.9 28.9 - - + -
151E VAL* 4.0 11.0 - - + -
153E ILE* 5.7 1.1 - - + -
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Residues in contact with VAL 101 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9E ILE* 3.9 21.5 - - + -
10E ILE 2.7 20.2 + - - +
11E ALA* 3.7 23.5 - - + +
12E HIS 4.6 2.1 + - - -
20E LEU* 3.6 37.5 - - + +
99E LEU* 4.4 7.6 - - + +
100E LEU* 1.3 71.0 - - - +
102E VAL* 1.3 63.8 + - - +
103E ASP 4.2 1.1 + - - +
112E THR* 5.5 1.4 - - - +
129E VAL* 3.8 9.4 - - + +
131E ASN* 4.0 29.6 - - + +
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Residues in contact with VAL 102 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E LEU* 3.8 28.5 - - + +
101E VAL* 1.3 78.0 - - - +
103E ASP* 1.3 75.5 + - - +
104E ALA* 3.4 0.7 + - - -
107E GLY 3.7 4.7 - - - +
108E VAL* 3.6 35.4 - - + +
112E THR* 6.5 0.2 - - + -
129E VAL 3.0 10.7 + - - +
130E LEU* 3.5 4.3 - - - +
131E ASN* 3.0 23.6 + - - -
143E VAL* 3.7 15.5 - - + -
147E ILE* 3.9 27.1 - - + -
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Residues in contact with ASP 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E ILE* 4.3 18.5 - - + +
101E VAL* 4.2 2.0 + - - +
102E VAL* 1.3 77.8 - - - +
104E ALA* 1.3 73.1 + - - +
105E GLY 3.0 15.5 + - - -
106E GLN* 3.6 29.9 - - + +
107E GLY 3.4 18.3 + - - +
131E ASN* 3.6 14.5 - - - +
132E LYS* 3.9 15.4 - - - +
135E LEU* 3.8 22.4 - - - +
143E VAL* 4.0 1.9 - - - +
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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