Contacts of the strand formed by residues 97 - 105 (chain B) in PDB entry 3IJE
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 SER 97 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B LEU* 3.8 3.8 - - - -
96B ASP* 1.3 91.3 + - - +
98B LYS* 1.3 73.1 + - - +
400B GLU* 3.5 23.4 + - - +
401B ALA 3.2 14.1 - - - -
402B LYS* 3.6 22.2 - - - +
3099B NAG 6.0 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B VAL* 4.2 7.7 - - - +
59B SER* 3.0 45.5 + - - +
60B GLU* 4.1 12.3 - - - +
61B ALA* 4.4 8.5 - - + +
90B LEU* 4.1 19.5 - - + +
92B LEU* 3.8 3.4 - - + +
96B ASP* 5.4 0.4 + - - -
97B SER* 1.3 80.5 - - - +
99B ASN* 1.3 65.3 + - - +
100B PHE* 4.2 4.8 - - - -
400B GLU* 4.6 3.1 - - - -
401B ALA* 3.1 31.5 + - - +
3099B NAG 4.3 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 4.6 8.3 - - - +
98B LYS* 1.3 78.6 - - - +
100B PHE* 1.3 67.3 - - - +
398B SER* 5.1 1.6 - - - +
399B ILE 3.1 14.8 - - - +
400B GLU* 4.1 10.3 - - + +
3099B NAG 1.4 91.0 + - - +
1K NAG 5.2 3.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B ALA* 4.9 9.4 - - + +
88B ILE* 3.6 31.0 - - + -
90B LEU* 4.9 9.2 - - + -
98B LYS 4.2 5.6 - - - -
99B ASN* 1.3 81.9 - - - +
101B SER* 1.3 62.8 + - - +
368B LEU* 5.2 1.3 - - + -
398B SER* 3.5 5.5 + - - -
399B ILE* 2.6 85.2 + - + +
401B ALA* 4.4 20.6 - - + -
414B PHE* 5.4 0.7 - + - -
416B ILE* 4.0 10.5 - - + -
425B LEU* 3.7 22.4 - - + -
427B VAL* 4.4 13.5 - - + -
3099B NAG 5.8 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B PRO* 3.5 18.0 - - - +
88B ILE* 5.6 1.2 - - - +
100B PHE* 1.3 85.7 - - - +
102B ILE* 1.3 64.5 + - - +
103B GLN* 3.8 16.2 + - - -
396B SER* 4.7 5.4 - - - -
397B PHE 3.2 15.7 - - - -
398B SER* 4.4 5.2 - - - -
399B ILE* 4.6 0.4 - - - +
425B LEU* 4.7 0.9 - - - +
3099B NAG 6.0 2.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B VAL* 3.3 33.9 - - + -
85B PRO* 4.0 7.0 - - + -
101B SER* 1.3 79.8 - - - +
103B GLN* 1.3 67.5 + - - +
104B VAL* 3.7 13.7 + - + -
357B LEU* 4.7 13.0 - - + -
396B SER* 3.6 1.4 - - - -
397B PHE* 3.1 46.6 + - + +
399B ILE* 4.0 17.9 - - + -
416B ILE* 4.0 12.8 - - + +
417B LYS* 5.5 0.2 - - - -
425B LEU* 3.7 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.5 19.7 - - + +
83B VAL* 3.4 5.5 - - - -
84B SER* 3.0 39.7 + - - -
85B PRO* 4.0 7.5 - - - +
101B SER* 3.8 13.9 + - - +
102B ILE* 1.3 89.8 + - - +
104B VAL* 1.3 60.7 + - - +
394B THR* 4.4 5.4 - - + -
395B VAL 3.6 6.5 - - - +
396B SER* 4.4 17.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
82B GLN 3.3 5.4 - - - +
83B VAL* 4.5 2.9 - - + -
102B ILE* 3.7 13.0 + - + -
103B GLN* 1.3 75.0 - - - +
105B ARG* 1.3 64.5 + - - +
355B VAL* 3.6 26.9 - - + -
357B LEU* 4.2 11.4 - - + -
394B THR* 3.2 3.2 - - - +
395B VAL* 2.8 38.8 + - + +
397B PHE* 4.2 20.9 - - + -
418B PRO* 3.6 29.2 - - + -
421B PHE* 3.7 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU* 3.4 35.1 + - + +
70B SER 3.0 27.4 + - - -
71B ASP* 4.5 10.0 + - - +
81B THR 4.8 0.2 - - - -
82B GLN* 2.9 35.1 + - - +
104B VAL* 1.3 76.8 - - - +
106B GLN* 1.3 66.8 + - - +
107B VAL* 3.4 23.9 + - + +
392B GLY* 3.5 15.6 + - - -
393B ASP 3.6 4.7 - - - +
394B THR* 3.2 30.4 + - + +
421B PHE* 3.5 13.0 - - - -
----------------------------------------------------------
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