Contacts of the strand formed by residues 93 - 101 (chain B) in PDB entry 1D02
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 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLU* 3.5 2.1 - - - -
88B ASN 3.0 25.3 + - - -
91B THR* 3.1 21.4 + - - +
92B HIS* 1.3 80.8 - - - +
94B ILE* 1.3 59.5 + - - +
138B GLY 3.1 13.2 - - - +
139B GLY* 3.6 24.1 + - - +
140B ILE* 5.0 0.9 - - + +
142B ASP* 5.1 7.5 + - - -
200B TYR 3.6 15.6 + - - +
201B LEU* 3.7 22.7 - - + +
202B ASP* 2.9 31.1 + - - +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 3.6 34.8 - - + +
85B ALA* 3.7 21.5 - - + -
86B ILE 3.4 10.8 - - - +
87B GLU* 3.8 25.8 - - + +
92B HIS 3.8 7.4 - - - +
93B LYS* 1.3 80.4 - - - +
95B LEU* 1.3 63.9 + - - +
96B PHE* 3.7 26.5 + - + -
137B ILE* 4.8 9.6 - - + +
138B GLY* 2.9 30.1 + - - -
140B ILE* 3.6 11.4 - - - +
147B PRO* 4.7 1.4 - - - +
201B LEU* 3.8 4.0 - - - -
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Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B PHE* 5.2 1.8 - - + -
85B ALA* 3.1 3.8 - - - -
86B ILE* 2.8 43.1 + - + +
94B ILE* 1.3 73.5 - - - +
96B PHE* 1.3 64.5 + - - +
140B ILE* 4.4 8.5 - - + -
146B LEU 4.8 3.6 - - - +
147B PRO 3.7 25.8 - - - +
148B PHE 3.9 14.4 - - - +
149B TRP* 4.0 19.7 - - + -
193B PHE* 4.1 17.7 - - + -
197B LEU* 3.9 36.1 - - + +
201B LEU* 3.8 15.0 - - + +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46B PRO* 4.3 3.4 - - + -
48B HIS* 3.7 42.4 - + + -
49B LEU* 3.9 22.0 - - + -
82B PRO* 4.1 11.4 - - + -
84B PHE* 3.8 2.0 - - - -
85B ALA* 3.8 13.7 - - + -
94B ILE* 3.7 27.4 - - + -
95B LEU* 1.3 75.9 - - - +
97B GLY* 1.3 59.3 + - - +
98B GLU* 5.9 0.2 - - - -
125B LEU* 6.3 0.2 - - - -
134B TYR* 3.4 41.3 - + + +
137B ILE* 3.9 11.7 - - + -
138B GLY* 4.0 22.2 - - - -
147B PRO 3.6 5.9 + - - -
148B PHE* 3.2 8.7 - - - +
149B TRP 3.0 21.8 + - - -
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B PRO* 3.6 1.2 - - - +
83B ALA 3.1 22.5 + - - -
84B PHE* 2.7 39.6 + - - +
95B LEU 4.0 0.2 + - - -
96B PHE* 1.3 76.5 - - - +
98B GLU* 1.3 70.4 + - - +
125B LEU* 5.7 0.2 - - - -
148B PHE* 5.4 0.7 - - - -
149B TRP 3.2 11.2 - - - -
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Residues in contact with GLU 98 (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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81B SER 4.7 1.9 - - - +
82B PRO* 3.4 19.0 - - - +
83B ALA* 3.4 18.2 + - - +
84B PHE* 3.5 4.2 - - - -
96B PHE* 6.1 0.2 - - - +
97B GLY* 1.3 80.8 - - - +
99B ILE* 1.3 69.5 + - - +
100B LYS* 4.2 19.4 + - + +
122B SER* 5.2 5.2 - - - -
124B LYS* 6.5 0.9 - - - -
125B LEU* 3.5 29.3 - - + +
134B TYR* 3.8 12.5 + - - -
149B TRP 3.0 6.1 + - - -
150B VAL* 4.2 17.0 - - + -
151B VAL 2.9 24.1 + - - -
3C C 5.4 2.9 - - - +
4C A 4.8 3.8 + - - -
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Residues in contact with ILE 99 (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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27B LEU* 4.0 26.2 - - + -
28B TYR* 3.7 35.9 - - + +
83B ALA* 3.8 10.4 - - + +
84B PHE* 3.9 13.9 - - + -
98B GLU* 1.3 82.3 + - - +
100B LYS* 1.3 74.4 + - - +
101B ARG* 3.8 32.1 + - + +
151B VAL* 3.2 7.6 - - + +
153B GLU* 3.7 32.5 - - - +
4C A 3.6 10.6 + - - +
5C A 5.4 0.2 + - - -
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Residues in contact with LYS 100 (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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98B GLU* 4.3 18.8 + - + +
99B ILE* 1.3 86.5 + - - +
101B ARG* 1.3 62.3 + - - +
102B GLN* 4.0 1.5 + - - +
118B ALA 5.0 0.7 - - - +
119B HIS* 4.3 19.7 - - + +
121B ARG* 4.0 17.7 - - - +
122B SER* 3.8 40.4 - - - +
150B VAL* 4.3 7.2 - - + -
151B VAL 2.8 9.6 + - - +
152B PHE* 3.2 28.1 - - + +
153B GLU 2.9 23.3 + - - +
156B ILE* 4.7 0.9 - - - +
4C A 3.1 30.3 + - - -
5C A 6.1 2.2 - - + -
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Residues in contact with ARG 101 (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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28B TYR* 5.1 8.5 + - - -
99B ILE* 3.8 35.4 + - + +
100B LYS* 1.3 75.2 - - - +
102B GLN* 1.3 67.1 + - - +
153B GLU* 3.3 38.1 + - + +
154B GLY* 5.5 1.1 - - - -
4C A 4.3 13.9 + - - -
5C A 2.8 66.0 + - - +
6C T 4.9 1.3 - - - +
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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