Contacts of the strand formed by residues 103 - 108 (chain B) in PDB entry 4U7C
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 ILE 103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ASN* 4.6 2.5 - - + -
102B THR* 1.3 75.8 - - - +
104B VAL* 1.3 67.2 + - - +
201B TYR* 4.5 4.3 - - + -
202B LEU 3.3 4.3 - - - +
203B ASN* 3.6 34.5 - - + +
312B GLY 3.5 1.0 - - - +
313B ILE* 3.4 4.2 - - - +
314B ALA 2.9 39.7 + - - +
315B PRO 3.9 17.5 - - - +
316B ASN* 4.2 8.1 - - - -
317B THR* 4.0 22.9 - - + +
320B ALA* 3.8 16.7 - - + +
405B THR* 4.0 15.0 - - - +
407B LEU* 3.7 21.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 4.7 0.2 - - + -
103B ILE* 1.3 81.8 - - - +
105B HIS* 1.3 65.3 + - - +
106B ILE* 3.8 26.7 - - + -
200B ALA 3.7 0.5 - - - +
201B TYR* 3.3 6.8 - - - +
202B LEU* 2.8 41.7 + - + +
204B ILE* 3.6 39.7 - - + -
294B VAL* 3.8 26.2 - - + -
297B ILE* 5.5 1.3 - - + -
311B ALA* 4.5 4.3 - - + -
312B GLY 3.1 7.9 - - - +
313B ILE* 4.4 7.9 - - + -
320B ALA* 4.5 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 1.3 75.4 - - - +
106B ILE* 1.3 59.7 + - - +
107B ASP* 3.7 20.8 - - + +
199B GLU* 3.3 25.1 + - + +
200B ALA 3.4 18.4 - - - -
201B TYR* 3.5 32.9 - + + -
311B ALA* 3.1 6.3 - - - -
312B GLY 2.9 31.4 + - - -
320B ALA* 3.9 21.5 - - + +
321B LYS* 3.4 30.5 + - + +
324B SER* 2.9 28.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B VAL* 3.8 18.2 - - + -
105B HIS* 1.3 73.6 + - - +
107B ASP* 1.3 61.0 + - - +
108B MET* 4.2 1.6 - - - -
181B VAL* 6.3 0.2 - - + -
185B LEU* 3.7 28.9 - - + -
198B ASP 3.7 0.6 - - - +
199B GLU* 3.2 6.2 - - - +
200B ALA 2.9 31.1 + - - +
202B LEU* 3.5 28.7 - - + -
294B VAL* 5.9 1.3 - - + -
297B ILE* 4.2 15.5 - - + -
298B ARG* 5.0 5.6 - - + -
301B ILE* 4.4 13.0 - - + -
309B ALA* 4.0 17.9 - - + -
310B SER 3.4 12.6 - - - +
311B ALA* 4.3 8.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B HIS* 3.7 13.7 - - + -
106B ILE* 1.3 75.0 - - - +
108B MET* 1.3 62.6 + - - +
198B ASP* 3.4 5.8 - - - +
199B GLU* 3.1 30.2 - - - +
309B ALA* 4.2 1.6 - - - -
310B SER 2.9 35.0 + - - +
321B LYS* 4.3 3.3 + - - -
324B SER* 4.3 5.7 + - - +
325B ASP* 4.5 5.2 - - - +
328B LYS* 3.1 25.0 + - - +
602B MG 2.0 33.4 - - - -
603B 0KX 3.3 4.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ILE* 6.0 1.1 - - - -
107B ASP* 1.3 69.6 - - - +
109B ASP* 1.3 60.7 + - - +
111B PHE* 3.9 20.4 - - + -
114B ALA* 6.2 0.2 - - + -
181B VAL* 4.3 25.6 - - + -
197B LEU 5.0 0.9 - - - +
198B ASP* 2.9 40.4 + - + +
301B ILE* 4.2 13.5 - - + -
305B THR* 4.9 1.1 - - - +
307B LEU* 3.6 36.6 - - + +
308B THR 3.4 21.3 - - - +
309B ALA* 3.8 16.8 - - - -
602B MG 2.7 26.5 - - - -
603B 0KX 3.1 7.4 + - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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