Contacts of the helix formed by residues 112 - 124 (chain B) in PDB entry 3C0M
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 PHE 112 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.1 43.1 - - + +
106B VAL* 3.4 22.9 - - + -
108B ASP* 2.9 9.8 + - + +
110B ALA 3.5 0.6 - - - -
111B ASN* 1.3 82.3 - - - +
113B ILE* 1.3 61.8 + - + +
114B LYS 3.4 1.1 - - - -
115B PRO* 3.4 2.3 - - - +
116B THR* 2.7 63.4 + - + +
151B ILE* 3.9 14.4 - - + -
170B ILE* 5.1 0.2 - - + -
172B VAL* 3.3 37.9 - - + -
314B TYR* 3.6 28.0 - + - -
316B LEU* 4.2 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B VAL 3.3 22.4 - - - +
107B HIS* 3.8 27.4 - - + +
108B ASP 2.8 14.7 + - - +
109B SER* 3.9 13.9 - - - +
112B PHE* 1.3 73.8 - - + +
114B LYS* 1.3 62.5 + - - +
116B THR* 3.3 4.7 + - - -
117B SER* 2.7 34.3 + - - +
137B GLY 3.9 17.5 - - - +
140B MET* 3.9 32.3 - - + +
142B VAL* 5.3 7.2 - - + -
151B ILE* 4.1 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLU* 2.8 33.9 + - - +
109B SER* 2.8 33.0 + - - +
110B ALA* 4.5 4.5 - - - +
113B ILE* 1.3 77.2 - - - +
115B PRO* 1.3 61.0 - - + +
117B SER* 3.5 4.2 - - - -
118B TYR* 3.0 47.6 + - + -
135B TYR* 4.2 1.8 - - - +
136B VAL 2.9 25.5 + - - +
137B GLY 3.8 11.9 - - - +
138B GLU* 2.6 39.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B SER 3.4 2.2 - - - +
110B ALA 3.2 23.8 - - - +
111B ASN 3.9 12.6 - - - +
112B PHE 3.4 12.3 - - - +
114B LYS* 1.3 95.8 - - + +
116B THR* 1.3 61.9 + - + +
118B TYR* 4.6 1.1 - - + -
119B LEU* 3.1 19.6 + - - +
388B ASN* 3.1 18.6 + - - +
391B ARG* 3.8 30.5 - - + -
392B VAL* 3.7 12.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PHE* 2.7 52.9 + - + +
113B ILE* 3.3 5.7 + - - -
115B PRO* 1.3 74.1 - - + +
117B SER* 1.3 67.1 + - - +
119B LEU* 3.2 10.6 + - - +
120B ALA* 3.1 21.5 + - - +
151B ILE* 6.0 1.0 - - - +
170B ILE* 4.0 25.6 - - - +
316B LEU* 3.9 26.9 - - + -
318B LEU* 4.8 2.0 - - - +
392B VAL* 4.5 13.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ILE* 2.7 28.1 + - - +
114B LYS 3.2 4.0 + - - -
116B THR* 1.3 76.0 + - - +
118B TYR* 1.3 60.0 + - - +
120B ALA* 3.1 6.3 + - - +
121B HIS* 2.8 27.2 + - - +
128B VAL* 3.5 17.7 - - - +
136B VAL* 4.1 2.5 - - - -
137B GLY* 3.5 30.8 - - - -
140B MET* 3.8 14.7 - - - +
151B ILE* 5.2 0.5 - - - +
170B ILE* 4.6 6.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415A GLU* 2.7 40.4 + - + +
416A ILE* 4.8 6.5 + - + -
114B LYS* 3.0 47.0 + - + +
115B PRO* 4.9 0.4 - - + -
117B SER* 1.3 73.9 - - - +
119B LEU* 1.3 61.2 + - - +
121B HIS* 3.5 8.7 - + - +
122B TYR* 2.7 68.7 + + + -
135B TYR* 5.2 0.7 - - - +
136B VAL* 3.4 37.7 + - + +
388B ASN* 3.6 17.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO 3.1 13.8 + - - +
116B THR* 3.3 11.7 - - - +
117B SER 3.1 0.2 - - - -
118B TYR* 1.3 78.1 - - - +
120B ALA* 1.3 62.7 + - - +
122B TYR* 3.2 2.7 + - + +
123B LEU* 2.9 40.9 + - + +
316B LEU* 4.5 9.4 - - + -
318B LEU* 4.3 12.3 - - + -
343B PHE* 4.3 15.5 - - + -
355B ILE* 4.2 12.6 - - + -
373B TRP* 4.4 7.0 - - + -
385B MET* 5.4 2.7 - - + -
388B ASN* 3.4 11.6 + - - +
389B LEU* 3.6 28.0 - - + -
392B VAL* 4.2 24.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B THR 3.1 8.9 + - - +
117B SER 3.4 8.5 - - - +
119B LEU* 1.3 80.4 - - - +
121B HIS* 1.3 61.6 + - - +
123B LEU* 3.4 0.8 + - - -
124B GLY 3.4 4.5 + - - -
125B TYR* 3.0 49.6 + - + +
128B VAL* 4.2 7.6 - - + -
168B THR* 4.7 2.2 - - + -
170B ILE* 3.9 20.6 - - + -
318B LEU* 4.2 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B SER 2.8 12.9 + - - +
118B TYR* 3.5 18.8 - + - +
120B ALA* 1.3 78.3 - - - +
122B TYR* 1.3 88.3 + + - +
124B GLY* 3.1 15.2 + - - -
125B TYR 4.2 12.9 + - - +
128B VAL* 4.2 8.1 - - + +
136B VAL* 4.1 24.3 - - + +
323B ARG* 5.6 13.8 + - - -
380B ASN* 5.5 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B TYR* 2.7 55.8 + + + +
119B LEU* 3.7 4.0 - - - +
121B HIS* 1.3 92.1 - + - +
123B LEU* 1.3 62.0 + - + +
124B GLY 3.6 0.3 + - - -
375B TRP* 3.8 12.8 - - - -
376B THR* 3.7 15.3 - - + +
380B ASN* 3.3 37.4 + - + +
384B THR* 3.5 25.0 - - + +
385B MET* 4.0 25.8 - - + -
388B ASN* 3.6 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B LEU* 2.9 22.9 + - + +
120B ALA 3.9 5.2 - - - +
121B HIS 3.1 0.2 - - - -
122B TYR* 1.3 81.5 - - + +
124B GLY* 1.3 58.4 + - - +
125B TYR* 3.7 6.3 - - + -
318B LEU* 4.0 13.9 - - + -
322B LEU* 4.3 1.9 - - - +
327B ASN 5.0 0.2 - - - -
328B ALA* 3.2 28.0 + - + +
343B PHE* 3.8 30.7 - - + -
371B TRP* 3.5 48.2 - - + -
373B TRP* 3.8 30.1 - - + -
376B THR* 4.4 10.3 - - + -
385B MET* 5.5 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B HIS 3.1 11.1 + - - -
122B TYR 3.3 1.4 + - - -
123B LEU* 1.3 80.0 - - - +
125B TYR* 1.3 65.2 + - - +
322B LEU* 3.5 9.4 - - - -
323B ARG* 2.7 34.2 + - - +
326B GLY 3.9 17.5 - - - -
327B ASN* 4.3 4.0 - - - -
375B TRP* 5.6 0.9 - - - -
----------------------------------------------------------
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