Contacts of the strand formed by residues 138 - 143 (chain B) in PDB entry 4CYM
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 ALA 138 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA* 3.4 12.6 - - + +
104B VAL* 4.7 5.8 - - + -
121B LYS* 3.8 31.9 - - + +
124B LEU* 4.7 3.8 - - + -
136B ILE 3.3 7.1 + - - +
137B PRO* 1.3 72.4 - - - +
139B VAL* 1.3 66.8 + - - +
166B GLY 4.4 4.2 + - - +
167B PHE* 3.6 14.6 - - + -
168B ALA* 2.9 30.2 + - - +
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Residues in contact with VAL 139 (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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102B ALA 2.9 7.7 + - - +
103B PHE* 3.4 29.3 - - + -
104B VAL 3.2 20.4 + - - +
138B ALA* 1.3 80.4 - - - +
140B LEU* 1.3 73.4 + - - +
141B LEU* 4.2 1.3 - - + -
167B PHE* 4.1 2.7 - - - -
168B ALA* 4.7 3.1 - - + -
169B GLY 4.1 7.9 - - - -
171B PHE* 3.9 27.1 - - + -
184B ALA* 4.8 0.9 - - + +
187B PHE* 3.8 26.9 - - + -
188B LEU* 3.9 26.7 - - + -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.4 19.7 - - + +
106B PHE* 3.8 32.8 - - + -
114B PHE* 4.5 3.4 - - + -
117B VAL* 4.4 16.4 - - + -
139B VAL* 1.3 73.3 - - - +
141B LEU* 1.3 69.2 + - - +
142B ALA 4.2 0.7 - - - +
158B VAL* 4.5 9.2 - - + -
161B PHE* 4.1 22.2 - - + -
162B CYS* 4.1 18.4 - - - -
167B PHE* 3.8 22.2 - - + -
169B GLY 3.3 16.8 + - - +
170B TRP* 3.2 28.9 - - + -
171B PHE 3.3 1.4 + - - -
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Residues in contact with LEU 141 (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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30B VAL* 6.1 0.2 - - + -
41B ILE* 3.9 31.4 - - + -
103B PHE* 3.9 33.4 - - + -
104B VAL 2.9 13.4 + - - +
105B VAL* 3.5 14.4 - - + +
106B PHE* 3.0 30.3 + - - -
139B VAL* 4.2 4.9 - - + +
140B LEU* 1.3 84.6 - - - +
142B ALA* 1.3 60.6 + - - +
143B ASN 3.3 3.3 + - - -
171B PHE* 3.7 5.2 - - + -
173B THR* 3.9 22.2 - - + +
181B ILE* 6.2 0.7 - - + -
184B ALA* 3.9 27.4 - - + -
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Residues in contact with ALA 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B PHE* 3.5 30.6 - - + -
108B ILE* 3.9 21.5 - - + -
140B LEU* 4.2 0.6 - - - +
141B LEU* 1.3 67.6 - - - +
143B ASN* 1.3 63.1 + - - +
145B CYS* 4.4 3.3 - - - +
170B TRP* 4.5 15.2 - - + -
171B PHE 2.9 13.9 + - - +
172B GLU* 3.4 7.4 - - - +
173B THR* 2.8 25.8 + - - +
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Residues in contact with ASN 143 (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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36B VAL 3.2 20.0 + - - +
37B GLY* 3.8 4.8 - - - -
41B ILE* 3.9 14.9 - - - +
105B VAL* 4.0 11.9 - - + -
106B PHE 2.8 17.0 + - - +
107B ASP* 3.9 0.3 - - - -
108B ILE* 3.0 22.3 + - - +
142B ALA* 1.3 72.7 - - - +
144B LYS* 1.3 81.8 + - - +
145B CYS 3.4 0.4 - - - -
173B THR* 2.7 27.1 + - - +
175B ALA 3.5 14.2 + - - -
1198B GCP 3.0 32.3 + - - -
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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