Contacts of the strand formed by residues 112 - 117 (chain I) in PDB entry 5A31
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 CYS 112 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I CYS* 3.4 8.3 - - - -
110I VAL* 3.5 4.6 - - - +
111I SER* 1.3 82.3 - - - +
113I MET* 1.3 71.0 + - - +
114I HIS* 5.5 0.9 - - - -
178I LEU* 3.6 2.4 - - - -
179I GLY 2.9 29.6 + - - +
205I CYS 3.2 16.6 - - - +
206I LEU 3.6 24.7 - - - +
207I ALA* 3.9 1.3 - - - -
208I LEU* 3.7 33.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 113 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I CYS* 3.6 34.8 - - + +
71I LEU 4.7 4.3 - - - +
72I ALA* 3.9 21.1 - - + +
81I ALA* 3.6 36.3 - - + +
82I PHE 4.2 0.2 - - - +
83I ALA* 3.9 12.8 - - + -
90I ILE* 3.9 24.0 - - + -
110I VAL* 4.5 4.5 - - + -
112I CYS* 1.3 82.6 - - - +
114I HIS* 1.3 59.7 + - - +
176I LEU* 4.1 7.9 - - + -
177I VAL 3.2 6.7 - - - +
178I LEU* 3.6 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 114 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ALA* 5.3 0.7 - - - -
112I CYS* 5.5 0.9 - - - -
113I MET* 1.3 74.6 - - - +
115I TRP* 1.3 77.2 + - - +
116I MET* 3.9 18.7 + - + +
176I LEU* 4.2 1.6 - - - -
177I VAL* 2.8 39.5 + - + +
208I LEU* 3.2 38.4 + - + +
209I CYS* 4.5 4.6 - - - -
210I LEU* 3.9 27.4 + - - +
575I LEU 5.5 5.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 115 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ALA* 4.3 8.4 - - + +
73I TRP 3.7 17.0 - - - +
74I ARG* 3.6 44.4 - - + +
75I PRO* 3.6 16.7 - - + +
79I LEU* 4.1 15.0 - - + -
81I ALA* 3.5 26.7 - - + -
92I LEU* 4.1 14.6 - - + -
114I HIS* 1.3 86.7 + - - +
116I MET* 1.3 72.0 + - - +
174I ASN* 3.5 25.0 - - - +
175I ILE 3.0 25.1 + - - -
176I LEU* 3.3 41.6 - - + +
190I TYR 4.1 13.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 116 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75I PRO* 3.8 7.2 - - - -
114I HIS* 3.9 15.4 + - + +
115I TRP* 1.3 76.6 - - - +
117I GLU* 1.3 74.4 + - - +
118I VAL 4.8 0.9 - - - +
174I ASN* 3.2 23.2 - - - +
175I ILE* 2.9 29.4 + - + +
177I VAL* 5.2 1.1 - - + -
210I LEU* 3.1 45.8 - - - +
211I SER 2.8 32.1 - - - +
212I SER* 4.3 2.2 - - - +
214I LEU* 3.5 18.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 117 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I LYS* 4.1 12.1 + - - -
75I PRO* 3.2 32.4 - - + +
76I ASP* 3.6 13.9 - - - +
116I MET* 1.3 88.5 - - - +
118I VAL* 1.3 69.6 + - - +
119I THR 4.0 0.3 + - - -
172I ARG* 3.1 36.9 + - + +
173I LEU 3.7 11.0 - - - +
174I ASN* 4.4 6.3 - - + -
212I SER* 4.5 8.3 - - - -
579I LYS* 4.2 25.2 + - - +
----------------------------------------------------------
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