Contacts of the strand formed by residues 57 - 62 (chain B) in PDB entry 1SNF
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 MET 57 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A GLY 4.6 3.1 - - - +
25A ALA* 5.3 0.5 - - - +
3B THR* 4.2 17.5 - - + -
53B VAL* 3.6 16.3 - - + +
54B PRO* 2.9 37.0 + - + +
55B PHE 4.8 1.3 - - - +
56B GLY* 1.3 82.7 + - - +
58B VAL* 1.3 62.4 + - - +
84B ALA* 4.2 10.9 + - - +
116B VAL* 3.8 20.2 - - + -
117B GLN 3.0 13.9 - - - +
118B ARG* 4.1 25.6 - - + +
119B VAL* 3.6 10.0 - - - +
120C GLU* 3.6 35.2 - - + +
122C VAL* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ALA* 3.5 28.9 - - + -
115A LEU* 4.5 5.2 - - + -
117A GLN* 4.0 8.7 - - - +
53B VAL* 3.7 8.3 - - - -
57B MET* 1.3 75.4 - - - +
59B GLY* 1.3 75.9 - - - +
60B LEU* 3.9 24.0 + - + +
81B THR* 3.8 12.1 - - + -
82B ILE 3.6 9.9 - - - +
83B ASP* 5.0 0.4 - - - +
115B LEU 3.7 0.2 - - - +
116B VAL* 3.3 4.7 - - - +
117B GLN 2.8 39.1 + - - +
119B VAL* 4.0 14.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B VAL* 3.7 12.8 - - - +
58B VAL* 1.3 81.4 - - - +
60B LEU* 1.3 61.1 + - - +
80B GLY 3.4 1.7 - - - +
82B ILE* 2.8 53.6 + - - -
114B LEU* 4.1 5.6 - - - -
115B LEU 3.3 7.9 - - - -
116B VAL* 4.7 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A HIS* 3.8 28.5 - - + +
115A LEU* 4.8 0.4 - - + -
117A GLN* 4.2 0.9 - - - +
58B VAL* 3.9 30.5 - - + +
59B GLY* 1.3 84.6 - - - +
61B VAL* 1.3 62.4 - - - +
62B HIS* 3.9 17.1 + - + +
79B PRO* 4.5 3.6 - - + -
80B GLY 3.2 7.9 - - - +
81B THR* 4.4 2.0 - - - +
113B GLN 3.6 1.4 - - - +
114B LEU* 3.3 5.0 - - - +
115B LEU* 2.8 44.9 + - + +
117B GLN* 3.0 33.2 - - + +
3174B TRS 3.2 21.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B LEU* 4.8 4.7 - - + -
60B LEU* 1.3 75.2 - - - +
62B HIS* 1.3 63.3 + - - +
75B ILE* 4.2 12.8 - - + +
78B SER* 3.9 3.3 + - - -
79B PRO* 3.3 8.0 - - - +
80B GLY* 2.9 43.6 + - - +
82B ILE* 4.0 21.1 - - + -
90B ILE* 4.3 11.9 - - + -
92B VAL* 4.4 13.9 - - + -
112B ALA* 3.8 24.5 - - + -
113B GLN 3.6 4.3 - - - +
114B LEU* 4.1 9.6 - - + -
2170B UMP 4.0 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B LEU* 3.9 11.5 - - + +
61B VAL* 1.3 82.4 - - - +
63B PRO* 1.3 73.8 - - + +
75B ILE* 3.7 3.8 - - - -
78B SER* 4.3 0.2 - - - -
79B PRO* 3.7 13.9 - - + -
112B ALA* 3.4 5.9 - - - +
113B GLN* 2.9 44.2 + - + -
115B LEU* 3.5 26.1 - - + +
3174B TRS 3.1 35.5 + - - -
60C LEU* 3.8 7.2 - - + -
79C PRO* 3.5 20.1 + - + +
81C THR* 2.8 25.3 + - - +
----------------------------------------------------------
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