Contacts of the strand formed by residues 136 - 140 (chain A) in PDB entry 5FJV
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 LYS 136 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A ARG* 3.7 12.2 + - + +
109A VAL 3.3 14.8 - - - +
110A PRO* 4.1 21.9 - - + +
111A SER 4.3 2.7 - - - +
135A THR* 1.3 88.3 + - - +
137A ALA* 1.3 63.3 + - - +
147A TRP* 3.5 4.2 - - - -
48E ALA 5.1 1.2 + - - -
49E ARG* 3.7 26.9 + - - +
115E TRP* 5.1 5.2 - - - +
116E ILE 5.6 4.5 - - - -
118E ASP* 5.0 10.9 + - + +
179E THR* 3.1 40.8 - - + +
180E TYR* 3.8 28.9 - - + +
300E EPJ 3.5 4.7 - - - +
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Residues in contact with ALA 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ARG* 3.7 5.4 - - - +
109A VAL* 2.7 39.0 + - + +
111A SER* 4.2 6.3 - - - +
114A ILE* 3.8 28.9 - - + -
116A ILE* 6.2 0.2 - - + -
135A THR 4.0 0.4 + - - -
136A LYS* 1.3 75.2 - - - +
138A HIS* 1.3 60.2 + - - +
139A LEU 3.6 1.6 + - - -
145A VAL* 3.8 14.4 - - + -
146A HIS 3.5 5.8 - - - +
147A TRP* 4.3 11.2 - - + -
300E EPJ 4.2 1.3 - - - -
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Residues in contact with HIS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A SER* 3.5 12.9 + - - -
107A LEU 4.2 4.0 - - - -
108A ARG* 2.9 49.4 + - + -
137A ALA* 1.3 71.7 - - - +
139A LEU* 1.3 61.0 + - - +
140A PHE* 3.1 40.3 + + - -
144A THR 3.6 2.8 - - - +
145A VAL* 4.7 0.7 - - - -
146A HIS* 2.7 50.6 + - + +
179E THR 5.6 0.2 - - - -
224E GLU* 3.9 22.1 + - + -
226E TYR* 5.1 0.4 + - - -
300E EPJ 3.8 15.7 - - + +
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Residues in contact with LEU 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.6 30.7 - - - +
94A LEU* 3.7 31.9 - - + +
96A TRP* 3.6 17.9 - - + -
106A SER* 3.3 5.4 - - - -
107A LEU* 3.2 33.6 + - + +
109A VAL* 4.0 20.6 - - + -
114A ILE* 5.5 0.7 - - + -
137A ALA 3.6 1.2 + - - -
138A HIS* 1.3 73.2 - - - +
140A PHE* 1.3 79.5 - - - +
143A GLY 3.9 13.5 - - - -
144A THR 3.3 13.9 - - - +
145A VAL* 4.3 12.6 - - + +
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Residues in contact with PHE 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A TRP* 3.4 3.5 - - - -
105A THR* 3.7 2.5 - - - +
106A SER* 3.1 20.6 - - - -
138A HIS* 3.1 42.0 - + - -
139A LEU* 1.3 85.3 - - - +
141A SER* 1.3 54.2 + - - +
142A THR* 2.8 20.3 + - + +
143A GLY 2.7 26.0 + - - -
144A THR* 3.0 14.9 + - - +
146A HIS* 3.6 35.7 - + - -
224E GLU* 4.7 7.2 - - - -
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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