Contacts of the helix formed by residues 93 - 106 (chain A) in PDB entry 7CE1
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 93 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU 4.8 1.6 + - - -
91A MET* 3.1 36.5 - - + +
92A GLY* 1.3 73.8 - - - +
94A THR* 1.3 65.2 + - - +
95A SER* 3.1 9.9 - - - +
96A GLN* 3.0 26.6 + - + -
294A SER 4.0 4.3 - - - +
295A ALA* 3.5 38.1 - - + -
297A PHE* 4.2 15.9 - + - -
312A ILE* 2.9 19.2 - - + +
90B LEU* 3.0 39.0 - - + -
91B MET* 4.1 22.0 - - + -
93B PHE* 5.7 9.9 - + - -
95B SER* 5.4 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 6.3 0.2 - - + -
84A LEU* 4.0 36.3 - - + -
88A GLU* 2.6 36.7 + - + +
92A GLY* 3.6 11.0 + - - -
93A PHE* 1.3 73.7 - - - +
95A SER* 1.3 57.5 + - - +
97A MET* 3.0 41.8 + - + +
98A VAL* 3.6 7.1 + - + +
312A ILE* 4.4 3.1 - - - -
95B SER* 3.9 13.3 + - - -
99B PHE* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 4.0 11.3 + - - +
94A THR* 1.3 79.7 - - - +
96A GLN* 1.3 65.2 + - - +
98A VAL* 3.2 21.9 + - - +
99A PHE* 3.3 21.9 + - - -
84B LEU* 5.9 1.6 - - - -
88B GLU* 3.1 26.6 + - - -
94B THR* 3.9 23.2 + - - -
95B SER* 4.1 13.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A PHE* 3.0 31.3 + - + +
95A SER* 1.3 78.0 + - - +
97A MET* 1.3 62.6 + - - +
99A PHE* 3.2 13.8 + - - +
100A GLY 3.1 9.2 + - - -
294A SER 5.2 3.8 - - - +
295A ALA* 5.5 4.7 - - + -
312A ILE* 3.5 15.9 - - + -
313A LYS* 2.9 51.3 - - + +
86B VAL 5.6 1.8 + - - -
88B GLU* 4.6 15.6 + - - +
90B LEU* 6.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 5.0 11.4 - - + -
84A LEU* 4.9 10.3 - - + -
94A THR* 3.0 30.0 + - + +
96A GLN* 1.3 78.3 - - - +
98A VAL* 1.3 63.9 + - + +
100A GLY 3.3 1.9 + - - -
101A ILE* 3.2 38.6 + - + +
140A ILE* 5.8 0.2 - - - -
142A SER* 5.2 9.0 - - - -
164A HIS* 4.0 26.2 - - + +
312A ILE* 3.9 26.9 - - + +
315A ALA* 5.1 0.2 - - - -
316A GLY* 3.5 11.3 - - - -
319A LEU* 3.6 26.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A LEU* 4.2 17.3 - - + -
84A LEU* 5.5 7.9 - - + -
94A THR* 3.9 13.9 - - + +
95A SER* 3.2 13.2 + - - +
97A MET* 1.3 76.7 - - + +
99A PHE* 1.3 65.9 + - + +
101A ILE* 3.2 12.2 + - - +
102A THR* 2.9 35.0 + - + +
112A LEU* 3.9 19.1 - - + -
114A VAL* 5.7 4.9 - - + -
84B LEU* 5.4 7.4 - - + -
98B VAL* 6.2 4.3 - - + -
114B VAL* 4.0 21.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 3.3 19.5 + - - -
96A GLN* 3.2 18.2 + - - +
98A VAL* 1.3 78.3 - - + +
100A GLY* 1.3 65.0 + - - +
102A THR* 3.0 10.9 + - + -
103A GLU* 2.9 31.3 + - - +
313A LYS* 4.7 11.0 - - + -
84B LEU* 3.9 37.0 - - + -
85B SER 3.4 17.5 - - - -
86B VAL* 3.5 43.7 - - + -
88B GLU* 3.8 26.0 - - - -
116B PRO* 4.5 10.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN 3.1 11.4 + - - -
97A MET 3.3 3.3 + - - -
98A VAL 3.3 0.2 - - - -
99A PHE* 1.3 76.9 - - - +
101A ILE* 1.3 61.2 + - - +
103A GLU* 3.7 2.3 + - - +
104A VAL* 3.3 15.1 + - - +
313A LYS* 3.4 30.4 - - - +
316A GLY 3.6 6.7 - - - -
317A ARG* 3.2 22.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 5.2 1.3 - - + -
82A LEU* 4.0 26.5 - - + -
97A MET* 3.2 24.0 - - + +
98A VAL* 3.2 7.7 + - - +
100A GLY* 1.3 73.7 - - - +
102A THR* 1.3 61.1 + - - +
104A VAL* 3.0 6.8 + - - +
105A LEU* 2.9 49.5 + - + +
112A LEU* 4.0 15.0 - - + -
140A ILE* 3.7 30.3 - - + -
316A GLY* 3.2 20.2 - - - +
319A LEU* 5.2 1.1 - - + -
320A ALA* 3.9 12.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A VAL* 2.9 21.0 + - + +
99A PHE* 3.0 20.8 + - + -
101A ILE* 1.3 72.7 - - - +
103A GLU* 1.3 65.4 + - - +
105A LEU* 3.7 8.5 - - + +
106A ALA* 2.9 24.9 + - - +
112A LEU* 3.8 13.2 - - + -
86B VAL* 6.1 0.2 - - - +
114B VAL* 3.8 27.8 - - + +
116B PRO* 3.3 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A PHE* 2.9 21.3 + - + +
100A GLY* 3.7 5.2 - - - +
101A ILE 3.2 0.2 - - - -
102A THR* 1.3 77.5 + - - +
104A VAL* 1.3 63.3 + - - +
106A ALA* 3.3 18.8 - - - +
107A THR* 4.6 4.0 + - - +
313A LYS* 3.4 29.2 + - - -
317A ARG* 4.0 20.1 + - + -
86B VAL* 4.6 12.8 - - + +
116B PRO* 5.3 0.2 - - - +
118B THR* 4.8 17.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A GLY 3.3 15.3 - - - +
101A ILE 3.0 7.7 + - - +
103A GLU* 1.3 78.2 - - - +
105A LEU* 1.3 62.0 + - - +
106A ALA 3.1 1.3 + - - -
107A THR* 3.8 18.4 + - - +
108A THR* 4.5 3.3 + - - +
317A ARG* 3.4 34.5 - - + +
320A ALA* 3.6 17.7 - - + -
321A LYS* 4.1 18.8 - - + -
324A LEU* 4.0 19.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ILE* 3.6 29.6 - - + -
101A ILE* 2.9 40.0 + - + +
102A THR* 3.2 7.8 + - + +
104A VAL* 1.3 77.9 - - + +
106A ALA* 1.3 62.9 + - - +
107A THR 3.3 0.2 - - - -
108A THR* 2.8 28.8 + - - +
110A TYR* 3.9 23.8 - - + +
111A HIS 4.5 10.8 - - - +
112A LEU* 4.0 26.7 - - + -
320A ALA* 4.9 2.5 - - + -
324A LEU* 4.0 19.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A THR 2.9 11.8 + - - +
103A GLU* 3.3 17.5 - - - +
104A VAL 3.1 0.6 - - - -
105A LEU* 1.3 78.4 - - - +
107A THR* 1.3 64.2 + - + +
108A THR 3.9 4.2 - - - +
----------------------------------------------------------
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