Contacts of the strand formed by residues 99 - 104 (chain A) in PDB entry 4J9D
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 TRP 99 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A PHE* 3.8 28.3 - + - -
75A SER* 4.9 0.9 - - - -
79A THR* 4.0 12.3 - - + -
93A TYR* 3.3 5.4 - - - -
94A ASN* 3.0 52.3 + - - +
98A GLU* 1.3 76.0 - - + +
100A CYS* 1.3 59.1 + - - +
110A TRP* 3.6 21.3 - - + -
111A VAL* 3.4 36.6 - - - -
112A PRO 3.8 2.9 - - - -
113A SER* 3.2 8.2 + - - -
1B ALA* 4.2 1.3 - - + -
2B PRO* 3.6 35.6 + - + -
4B TYR* 2.8 36.3 + + - -
5B PRO* 3.8 1.3 - - + -
6B PRO* 3.3 42.7 - - + +
7B PRO* 4.4 2.0 - - + -
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Residues in contact with CYS 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.6 26.5 - - - -
92A GLY 3.4 12.6 - - - -
93A TYR* 3.7 10.5 - - + -
99A TRP* 1.3 74.4 - - - +
101A GLU* 1.3 66.9 + - - +
102A ALA* 3.6 4.3 + - - -
110A TRP* 3.3 5.3 - - - -
111A VAL* 2.8 45.0 + - + +
113A SER* 3.6 19.1 - - - +
116A ILE* 3.6 22.0 - - + -
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Residues in contact with GLU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A VAL* 3.8 1.9 - - - -
91A LEU* 2.8 47.8 + - + +
92A GLY* 2.8 17.9 + - - +
100A CYS* 1.3 69.3 - - - +
102A ALA* 1.3 62.2 + - - +
108A GLN* 3.5 25.7 + - + +
109A GLY* 3.6 13.1 - - - +
110A TRP* 3.4 43.7 + - + -
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Residues in contact with ALA 102 (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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80A LEU* 3.9 3.5 - - + +
88A LEU* 3.8 27.8 - - + -
89A ARG 3.3 12.1 - - - +
90A VAL* 4.7 1.3 - - + -
91A LEU* 4.6 0.7 - - - +
100A CYS* 4.5 7.4 - - - +
101A GLU* 1.3 76.0 - - - +
103A GLN* 1.3 64.0 + - - +
108A GLN* 3.2 6.6 - - - +
109A GLY 2.9 35.1 + - - +
111A VAL* 4.3 15.9 - - + -
116A ILE* 5.2 0.2 - - + -
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Residues in contact with GLN 103 (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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88A LEU* 3.2 7.3 - - - -
89A ARG* 2.8 50.3 + - + +
91A LEU* 3.8 29.0 - - + +
102A ALA* 1.3 76.5 - - - +
104A THR* 1.3 64.0 + - - +
107A GLY 3.4 5.8 - - - +
108A GLN* 2.9 33.0 + - + +
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Residues in contact with THR 104 (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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80A LEU* 3.8 18.4 - - + +
81A SER 4.9 0.9 + - - -
82A ILE* 4.1 9.0 - - + -
86A GLU* 4.5 11.1 + - - +
87A LYS 3.8 13.2 - - - +
88A LEU* 3.7 31.0 - - + -
103A GLN* 1.3 82.3 - - - +
105A LYS* 1.3 65.3 + - - +
106A ASN* 3.0 25.2 + - - +
107A GLY* 2.9 19.6 + - - +
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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