Contacts of the strand formed by residues 103 - 107 (chain B) in PDB entry 3R27
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 103 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B SER* 3.0 8.4 + - - +
102B PRO* 1.3 78.9 - - - +
104B VAL* 1.3 62.4 + - - +
141B LEU* 4.3 11.9 - - + -
142B VAL 3.5 11.4 - - - +
143B GLU* 4.2 14.1 - - + +
173B TYR* 3.6 4.3 - - - -
174B SER* 2.7 42.4 + - - +
176B SER 3.3 23.1 - - - +
177B GLN 3.6 21.5 - - - +
178B LYS* 3.6 11.4 - - - +
179B ILE* 4.2 18.8 - - + +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 1.3 76.4 - - - +
105B HIS* 1.3 60.2 + - - +
106B ILE* 3.8 18.3 + - + -
122B LEU* 4.7 0.7 - - + -
141B LEU* 3.4 7.1 - - - +
142B VAL* 2.9 53.6 + - + +
144B PHE* 3.7 19.5 - - + -
150B ALA* 3.7 31.6 - - + +
153B ALA* 4.9 1.1 - - + -
154B VAL* 4.0 20.6 - - + -
171B VAL* 4.0 10.3 - - + -
172B ASN 3.4 8.3 - - - +
173B TYR* 4.5 1.6 - - + -
174B SER* 4.2 2.5 - - - -
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 1.3 71.4 - - - +
106B ILE* 1.3 65.8 + - - +
107B ARG* 3.6 24.7 - - + +
134B MET* 3.7 8.4 - - + +
139B GLN* 2.9 33.0 + - - -
140B ALA 3.4 16.4 - - - -
141B LEU* 3.7 19.3 - - + -
170B PHE 3.6 1.9 - - - +
171B VAL* 3.4 4.5 - - - -
172B ASN* 2.7 42.9 + - - +
174B SER* 4.1 6.3 - - - +
182B GOL 3.6 35.5 + - - +
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Residues in contact with ILE 106 (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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104B VAL* 3.8 9.4 - - + +
105B HIS* 1.3 73.7 - - - +
107B ARG* 1.3 63.6 + - - +
109B LEU* 3.8 25.8 - - + -
118B LEU* 4.5 5.4 - - + -
122B LEU* 3.6 27.4 - - + -
139B GLN* 3.1 9.7 - - - +
140B ALA* 2.8 43.5 + - + +
142B VAL* 3.9 18.4 - - + -
164B ILE* 4.3 8.5 - - + -
169B ALA* 3.9 16.2 - - + -
170B PHE 3.3 4.3 - - - +
171B VAL* 3.7 30.5 - - + -
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Residues in contact with ARG 107 (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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105B HIS* 3.6 31.9 - - + +
106B ILE* 1.3 80.7 - - - +
108B GLY* 1.3 64.2 + - - +
109B LEU 3.6 1.8 - - - -
139B GLN* 3.7 26.7 - - + +
169B ALA* 3.4 4.5 - - - +
170B PHE* 2.8 73.6 + - + +
171B VAL 4.3 0.2 - - - +
172B ASN* 3.1 34.4 - - - +
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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