Contacts of the strand formed by residues 3 - 9 (chain B) in PDB entry 4IGM
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 3 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B MET 3.6 0.4 + - - -
2B LYS* 1.3 80.2 - - + +
4B ASP* 1.3 67.7 + - - +
5B ILE* 4.5 2.5 - - + +
69B THR* 5.4 0.9 - - + -
70B VAL* 3.6 38.6 - - + +
72B ALA* 5.5 1.3 - - + +
288B LEU* 3.3 28.9 + - - +
320B LYS 2.7 17.1 + - - +
321B ALA* 4.0 15.5 - - + +
324B ALA* 3.7 26.0 - - + +
325B LEU* 3.6 40.2 - - + +
328B LEU* 5.4 8.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 4 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 1.3 73.7 - - - +
5B ILE* 1.3 59.6 + - - +
6B HIS 3.1 15.7 + - - +
7B SER* 4.5 4.5 - - - -
68B VAL* 4.0 19.7 - - + +
70B VAL 2.8 16.0 + - - +
71B GLN* 3.4 12.8 + - + +
72B ALA 2.8 26.7 + - - +
288B LEU* 3.8 5.6 - - + -
289B GLY* 3.5 0.8 - - - -
290B THR* 2.8 54.8 + - - +
292B TYR* 4.1 7.1 - - - +
301B PRO* 4.9 1.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ILE* 3.8 4.0 - - + +
4B ASP* 1.3 72.7 - - - +
6B HIS* 1.3 66.5 + - + +
7B SER 4.0 0.4 - - - -
72B ALA* 3.6 23.6 - - + +
114B LEU* 3.9 13.0 - - + +
172B PHE* 4.2 23.7 - - + -
221B CYS* 5.0 0.9 - - - -
265B ASP* 4.2 9.0 - - + -
287B ILE* 3.7 25.4 - - + -
288B LEU 3.1 19.6 + - - +
289B GLY* 4.2 3.1 - - - -
324B ALA* 4.8 5.4 - - + -
327B PHE* 3.7 34.3 - - + -
328B LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 6 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 3.1 11.5 + - - +
5B ILE* 1.3 82.4 - - + +
7B SER* 1.3 61.5 + - - +
8B HIS* 3.1 19.5 + + - -
74B SER* 6.0 0.4 - - - -
172B PHE* 3.9 12.1 - + + -
174B HIS* 3.2 9.6 + + - -
223B ALA* 4.0 8.3 - - + -
224B HIS* 3.7 21.5 - + - -
265B ASP* 2.7 25.6 + - - +
267B LEU* 4.1 4.5 - - + +
289B GLY* 3.7 6.5 - - - -
290B THR 3.7 11.2 - - - +
291B ASP* 2.8 41.1 + - + -
292B TYR 3.6 0.5 + - - -
401B ZN 2.3 29.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 7 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B ASP* 4.4 4.0 - - - -
6B HIS* 1.3 78.5 - - - +
8B HIS* 1.3 63.9 + - - +
59B ARG* 3.0 22.9 + - - -
71B GLN* 3.5 22.6 - - - +
72B ALA 3.2 15.9 + - - +
73B LEU* 3.5 2.6 - - - +
74B SER* 3.0 29.4 + - - -
292B TYR* 3.3 20.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 8 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B HIS* 3.1 13.4 + + - -
7B SER* 1.3 73.9 - - - +
9B ILE* 1.3 59.7 + - - +
53B CYS* 4.6 1.8 - - - +
59B ARG* 2.8 21.3 + - - -
74B SER* 3.1 12.7 + - - +
75B THR 3.0 18.2 + - - -
76B VAL* 3.9 22.4 - - + -
77B PRO* 3.9 6.5 - - + +
142B GLN* 3.1 24.9 - - - -
172B PHE* 5.3 0.2 - + - -
174B HIS* 3.5 7.2 - + - -
291B ASP* 3.0 10.1 + - - -
292B TYR 2.8 10.4 + - - +
293B PRO* 3.6 10.3 - - - +
294B PHE* 3.7 24.5 - + + -
401B ZN 2.2 35.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 9 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B HIS* 1.3 74.6 - - - +
10B LEU* 1.3 85.2 + - - +
53B CYS* 3.2 17.5 - - - +
54B TRP* 4.2 13.0 - - - +
56B PRO* 4.8 4.3 - - + -
59B ARG* 3.7 28.3 - - - +
73B LEU* 4.2 25.4 - - + -
74B SER 3.0 15.3 + - - +
75B THR* 3.7 13.9 + - - -
76B VAL* 3.8 3.1 + - - -
99B ASP* 5.7 3.1 - - - +
100B LEU* 3.6 30.3 - - + -
103B THR* 4.5 18.2 - - + +
111B PHE* 6.1 0.2 - - + -
----------------------------------------------------------
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