Contacts of the strand formed by residues 122 - 126 (chain B) in PDB entry 4JDL
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 GLU 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B LYS* 5.1 7.4 + - - +
90B ILE* 5.2 4.0 - - - +
106B LEU* 3.6 5.0 - - - +
107B ARG* 2.6 78.4 + - + +
109B VAL* 3.9 20.2 - - - +
120B SER* 2.9 31.9 + - - -
121B THR* 1.3 76.1 + - - +
123B ARG* 1.3 58.2 + - - +
136B PHE* 4.5 7.2 - - + +
137B SER 3.3 7.6 - - - +
138B VAL* 4.0 17.5 - - + +
139B VAL* 4.3 0.5 - - - +
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Residues in contact with ARG 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 3.6 4.7 - - - -
104B GLY* 4.0 32.8 - - - -
106B LEU* 3.9 13.0 - - - +
107B ARG 4.0 0.9 - - - +
122B GLU* 1.3 77.7 - - - +
124B LEU* 1.3 65.9 + - - +
125B GLU* 3.3 9.0 + - + +
136B PHE* 3.0 24.3 - - - +
137B SER* 2.9 28.3 + - - +
139B VAL* 4.0 30.0 - - + +
37C ARG* 4.7 11.1 - - - +
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Residues in contact with LEU 124 (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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78B ARG 5.7 0.2 - - - +
80B PHE* 3.1 56.2 - - + -
101B LEU 4.6 5.6 - - - +
102B HIS 3.3 25.8 - - - +
103B VAL* 3.5 5.3 - - - -
104B GLY* 2.4 36.0 + - - +
105B ASP 4.1 4.6 + - - +
123B ARG* 1.3 72.2 + - - +
125B GLU* 1.3 61.0 + - - +
126B ILE 3.6 28.3 - - - +
127B LEU* 3.4 31.4 - - + -
134B ILE* 6.3 0.4 - - + -
135B SER 4.1 4.0 - - - +
136B PHE* 5.5 0.2 - - + -
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Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B VAL* 4.9 6.8 - - - +
104B GLY* 4.9 0.4 - - - +
123B ARG* 3.3 11.8 + - - +
124B LEU* 1.3 74.6 - - - +
126B ILE* 1.3 68.4 + - + +
135B SER* 3.0 31.1 + - - +
136B PHE* 3.4 0.9 - - - -
137B SER* 2.9 40.8 + - - +
149B ARG* 2.5 42.2 + - - +
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Residues in contact with ILE 126 (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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48B HIS* 4.5 20.2 - - + +
103B VAL* 4.8 1.3 - - - -
124B LEU* 3.6 11.1 - - - +
125B GLU* 1.3 90.7 - - + +
127B LEU* 1.3 65.5 + - - +
128B ASP* 4.0 11.0 - - + +
133B VAL* 4.0 20.6 - - + -
134B ILE* 3.6 20.4 - - - +
135B SER* 3.6 31.1 + - - +
149B ARG* 4.2 13.5 - - - +
151B VAL* 4.8 3.1 - - + -
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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