Contacts of the strand formed by residues 98 - 102 (chain B) in PDB entry 2COJ
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 LEU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B GLU* 4.4 4.5 - - + -
97B GLY* 1.3 79.9 - - - +
99B LYS* 1.3 64.3 + - - +
110B LEU* 4.9 7.2 - - + -
111B PHE 5.2 4.9 - - - +
113B PRO* 5.4 8.5 - - + -
116B ASN* 3.8 29.8 - - + +
117B MET* 5.1 5.8 - - + -
138B LEU* 6.6 0.2 - - + -
141B ILE* 5.0 5.2 - - + -
161B TYR* 3.6 3.3 - - - -
162B ILE* 2.6 91.9 + - + +
164B PRO* 3.5 25.6 - - + -
333B THR* 4.2 5.6 - - - -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 1.3 83.0 - - - +
100B ALA* 1.3 61.2 + - - +
101B PHE* 3.5 37.1 - - + -
110B LEU* 3.3 26.0 - - - +
111B PHE* 3.8 6.6 + - - +
159B SER* 3.2 26.0 + - - +
160B LEU 3.3 8.1 - - - +
161B TYR* 4.3 10.3 - - + -
162B ILE* 4.3 1.6 - - - -
190B VAL* 4.0 15.7 - - - +
191B GLY 4.6 4.4 + - - -
333B THR* 3.0 45.0 + - + +
334B ALA* 3.1 21.7 + - - +
336B VAL* 5.0 6.5 - - - +
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 1.3 74.0 - - - +
101B PHE* 1.3 61.1 + - - +
108B ILE* 4.2 8.1 - - + -
109B ARG 3.3 6.7 - - - +
110B LEU* 3.8 15.0 - - + -
145B VAL* 4.2 17.7 - - + -
152B VAL* 3.8 6.6 - - + +
159B SER* 3.5 5.9 - - - -
160B LEU* 3.0 44.9 + - + +
162B ILE* 4.2 7.8 - - + +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LYS* 3.5 45.5 - - + -
100B ALA* 1.3 75.9 - - - +
102B ARG* 1.3 59.2 + - - +
103B GLY 3.4 3.0 + - - -
108B ILE* 3.2 1.7 - - - -
109B ARG* 2.7 44.0 + - - +
110B LEU 5.2 0.2 - - - -
111B PHE* 4.0 15.5 - - + -
152B VAL* 3.9 3.8 - - - -
159B SER* 3.8 18.6 - - - +
333B THR* 5.9 0.2 - - + -
336B VAL* 6.2 0.7 - - + -
373B GLN* 3.2 70.9 - - + +
374B TYR* 3.6 35.9 - + + -
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Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 1.3 69.6 - - - +
103B GLY* 1.3 74.4 - - - +
104B VAL* 4.6 0.9 - - - +
106B ASN* 3.1 38.0 + - - +
107B LYS 3.9 2.5 - - - -
108B ILE* 4.0 20.6 - - + +
149B GLN* 3.4 21.8 + - - +
150B GLU* 4.3 4.2 + - - +
152B VAL* 3.1 35.3 + - + +
153B PRO 3.4 17.6 + - - +
154B TYR* 3.3 55.3 + - - +
155B SER 4.7 4.3 - - - +
156B THR* 5.5 1.6 - - - +
158B ALA 5.6 0.6 + - - -
374B TYR* 3.3 19.8 - - - -
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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