Contacts of the strand formed by residues 102 - 107 (chain D) in PDB entry 2J3W
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 102 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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71D PHE* 4.1 2.9 - - - -
95D ASN 4.0 0.3 - - - +
96D TRP* 3.5 5.3 - - - -
97D SER* 2.8 40.3 + - - -
100D GLY 3.4 1.8 + - - -
101D ASP* 1.3 97.7 - - - +
103D PHE* 1.3 61.0 + - - +
164D ARG* 2.8 41.3 + - - +
165D MET 2.9 17.7 - - - +
166D ARG* 3.5 25.0 - - + +
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Residues in contact with PHE 103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71D PHE* 3.5 39.9 - + - -
75D ALA* 3.5 31.2 - - + -
78D ILE* 4.7 7.2 - - + -
93D ILE* 4.0 9.2 - - + -
94D THR 3.8 7.4 - - - +
95D ASN 4.3 0.4 - - - -
96D TRP* 3.7 36.6 - + + -
102D GLU* 1.3 73.9 - - - +
104D SER* 1.3 70.5 + - - +
105D LEU* 3.8 19.3 - - + -
164D ARG* 3.6 7.7 - - - +
165D MET* 2.6 70.7 + - + +
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Residues in contact with SER 104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D SER 3.4 0.7 - - - +
93D ILE* 3.4 6.6 - - - -
94D THR* 2.9 41.8 + - - -
95D ASN* 3.9 8.5 - - - +
103D PHE* 1.3 76.1 - - - +
105D LEU* 1.3 63.5 + - - +
106D ILE* 4.1 1.1 - - - -
162D GLU* 2.5 36.4 + - - +
163D ILE 3.5 3.1 - - - -
164D ARG* 2.8 29.5 + - - +
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Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75D ALA 5.3 0.4 - - - +
78D ILE* 4.3 9.0 - - + -
79D ALA* 3.6 30.7 - - + +
83D PHE* 4.2 26.5 - - + -
91D PRO* 4.2 11.9 - - + -
92D SER 4.5 0.9 - - - +
93D ILE* 4.0 16.6 - - + -
103D PHE* 3.8 16.4 - - + -
104D SER* 1.3 72.9 - - - +
106D ILE* 1.3 62.4 + - - +
107D LEU* 3.7 6.3 + - + +
135D LEU* 4.7 9.2 - - + -
161D THR 3.5 4.9 - - - +
162D GLU* 3.6 0.9 - - - -
163D ILE* 2.8 44.5 + - + +
165D MET* 4.2 18.2 - - + -
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Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D PRO* 3.2 8.2 - - - +
92D SER* 3.0 47.0 + - - +
94D THR* 3.7 23.8 - - + +
95D ASN* 4.9 2.7 - - - +
104D SER* 4.5 2.0 - - - -
105D LEU* 1.3 76.7 - - - +
107D LEU* 1.3 64.6 + - - +
108D GLU* 4.0 1.2 + - - +
152D GLN* 5.5 0.4 - - - +
160D VAL* 4.0 34.5 - - + -
161D THR 3.6 1.6 - - - +
162D GLU* 4.1 26.9 - - + +
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Residues in contact with LEU 107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83D PHE* 4.0 9.0 - - + -
89D ILE* 3.9 16.6 - - + -
91D PRO* 3.3 33.7 - - + -
105D LEU* 4.5 7.4 - - + +
106D ILE* 1.3 76.3 - - - +
108D GLU* 1.3 61.3 + - - +
110D ASN* 4.3 23.8 - - + +
131D LEU* 4.3 17.0 - - + -
150D PHE* 4.8 0.9 - - + -
160D VAL* 4.8 4.0 - - - +
161D THR* 3.0 48.2 + - + +
163D ILE* 4.0 25.4 - - + -
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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