Contacts of the helix formed by residues 103 - 119 (chain A) in PDB entry 1EG4
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 103 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 3.6 2.2 - - - +
102A ARG* 1.3 85.9 - - + +
104A SER* 1.3 61.1 + - - +
105A ALA* 3.3 1.6 - - + +
106A TYR* 3.0 35.5 + + + +
107A ARG* 2.8 27.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ARG 3.5 4.4 + - - -
103A PHE* 1.3 71.6 - - - +
105A ALA* 1.4 59.1 + - - +
107A ARG* 3.4 25.3 - - - +
108A THR* 2.8 35.3 + - - -
250A GLU* 4.9 0.4 - - - -
253A SER* 3.2 39.4 + - - -
254A PHE* 4.4 2.0 - - - -
290A GLN* 5.0 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 3.3 1.8 - - + +
104A SER* 1.4 81.1 + - - +
106A TYR* 1.4 62.6 + - + +
108A THR* 4.1 0.9 - - - -
109A ALA* 2.9 28.9 + - - +
254A PHE* 4.1 12.3 - - + -
290A GLN* 5.8 0.4 - - - +
293A VAL* 4.0 28.3 - - + +
294A TRP* 4.4 2.6 - - - +
297A VAL* 3.4 25.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101A VAL* 4.1 5.8 - - + -
103A PHE* 3.0 37.4 + + + +
105A ALA* 1.4 81.2 - - + +
107A ARG* 1.3 67.2 - - - +
109A ALA* 3.6 1.4 - - - +
110A MET* 2.9 43.7 + - + +
297A VAL* 3.6 22.0 - - + -
300A ARG* 3.0 40.2 + - + -
301A VAL* 4.7 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.2 29.1 - - + +
99A ASN* 3.9 21.4 + - - +
101A VAL* 3.0 45.2 + - + +
102A ARG 4.0 7.5 + - - -
103A PHE 2.8 14.4 + - - +
104A SER* 3.4 30.4 - - - +
106A TYR* 1.3 75.4 - - - +
108A THR* 1.4 62.7 + - - +
110A MET* 3.2 2.8 + - - +
111A LYS* 3.0 29.8 + - - +
250A GLU* 2.9 41.3 + - - +
253A SER* 4.5 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A SER 2.8 18.8 + - - -
105A ALA 4.1 1.1 - - - -
107A ARG* 1.4 76.3 - - - +
109A ALA* 1.4 62.9 + - - +
111A LYS* 3.2 11.3 + - - +
112A LEU* 2.9 35.0 + - + +
245A PRO* 3.9 14.1 - - + -
248A LEU* 4.2 9.9 - - + -
250A GLU* 3.4 24.3 + - + +
254A PHE* 3.4 30.2 - - + -
294A TRP* 3.9 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ALA 2.9 19.8 + - - +
106A TYR 3.6 3.1 - - - +
108A THR* 1.4 77.9 - - - +
110A MET* 1.3 57.0 + - - +
112A LEU* 3.4 6.2 + - - -
113A ARG* 2.8 29.5 + - - +
294A TRP* 4.0 7.5 - - - +
297A VAL* 3.5 11.4 - - + -
298A LEU* 3.4 39.4 - - - +
301A VAL* 3.7 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 3.8 23.0 - - + +
101A VAL* 4.0 34.1 - - + -
106A TYR* 2.9 37.5 + - + +
107A ARG* 3.7 4.0 - - - +
109A ALA* 1.3 70.2 - - - +
111A LYS* 1.3 67.1 + - - +
113A ARG* 3.2 8.7 + - - +
114A ARG* 3.0 23.2 + - - +
301A VAL* 3.9 22.4 - - + -
306A THR* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A LEU* 3.5 47.3 - - + +
98A LEU* 3.7 18.6 - - + +
99A ASN* 3.0 26.4 + - - +
107A ARG* 3.0 25.4 + - - +
108A THR* 3.2 8.5 + - - +
110A MET* 1.3 77.9 - - - +
112A LEU* 1.3 62.0 + - - +
114A ARG* 3.2 4.3 + - - +
115A LEU* 3.0 22.1 + - - +
248A LEU* 3.8 27.4 + - + -
250A GLU* 2.8 32.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A THR* 2.9 30.4 + - + +
109A ALA* 3.7 6.7 - - - +
111A LYS* 1.3 76.5 - - - +
113A ARG* 1.4 58.6 + - - +
115A LEU* 3.7 22.5 - - + +
116A GLN* 2.8 30.5 + - - +
181A TRP* 5.3 0.9 - - + +
206A LEU* 4.5 11.1 - - + +
244A ILE* 3.7 23.6 - - + +
245A PRO 5.4 0.9 - - - -
248A LEU* 3.6 21.8 - - + -
294A TRP* 3.4 40.2 - - + +
298A LEU* 4.3 12.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA 2.8 20.8 + - - +
110A MET* 3.5 6.1 - - - +
112A LEU* 1.4 74.1 - - - +
114A ARG* 1.3 64.4 + - - +
116A GLN* 2.8 34.5 + - - +
117A LYS* 3.1 45.0 + - - +
122A ASP* 3.8 16.0 + - - +
298A LEU* 3.8 12.5 - - + +
301A VAL* 4.1 11.7 - - + -
302A ALA* 3.5 32.3 + - - +
305A GLU 3.8 10.3 + - - -
306A THR* 2.9 37.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 3.9 16.8 - - + -
94A SER* 2.6 50.0 + - - -
95A LEU* 3.6 12.3 - - + +
97A ASP* 2.7 26.9 + - - -
98A LEU* 3.5 24.2 - - - +
110A MET 3.0 12.0 + - - +
111A LYS* 3.5 8.7 - - - +
113A ARG* 1.3 80.7 - - - +
115A LEU* 1.3 56.1 + - - +
117A LYS* 3.4 14.9 + - - +
118A ALA* 2.9 27.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.4 4.9 - - + -
91A LEU* 3.6 31.8 - - + +
92A TYR* 3.9 17.7 - - + +
95A LEU* 5.9 2.0 - - + -
111A LYS 3.0 15.7 + - - +
112A LEU* 3.7 16.4 - - + +
113A ARG 3.2 0.2 - - - -
114A ARG* 1.3 73.1 - - - +
116A GLN* 1.4 65.7 + - - +
118A ALA* 3.0 3.5 + - - +
119A LEU* 2.9 46.1 + - + +
181A TRP* 3.4 38.6 - - + +
206A LEU* 4.0 11.2 - - + -
248A LEU* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 2.8 21.5 + - - +
113A ARG* 2.8 41.9 + - - +
115A LEU* 1.4 73.9 - - - +
117A LYS* 1.3 56.8 + - - +
119A LEU* 3.4 3.6 + - - -
120A CYS 3.0 5.7 + - - -
121A LEU* 2.9 30.0 + - + -
122A ASP* 3.5 22.5 - - + +
206A LEU* 2.8 46.8 + - + +
207A CYS 3.4 14.8 + - - -
208A LYS* 4.6 2.4 - - - +
214A LYS* 5.1 0.4 - - - +
298A LEU* 4.3 15.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 3.1 49.4 + - - +
114A ARG* 3.8 15.5 - - - +
116A GLN* 1.3 75.3 - - - +
118A ALA* 1.3 67.5 + - - +
120A CYS* 3.0 18.7 + - - -
122A ASP* 3.6 29.6 - - + +
306A THR* 3.7 18.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.0 27.8 - - + -
114A ARG 2.9 17.8 + - - +
115A LEU 3.0 5.3 + - - +
117A LYS* 1.3 75.9 - - - +
119A LEU* 1.3 63.2 + - + +
120A CYS* 3.5 5.5 + - - -
174A CYS* 4.7 5.9 - - - -
177A MET* 4.9 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A MET* 4.5 4.9 - - - -
115A LEU* 2.9 44.3 + - + +
116A GLN 3.9 1.8 - - - +
118A ALA* 1.3 78.5 - - + +
120A CYS* 1.3 62.8 + - - +
121A LEU* 3.2 21.7 + - + -
158A TYR* 2.7 34.7 + - - +
174A CYS* 4.6 5.4 - - - +
177A MET* 3.7 34.5 - - + +
178A CYS* 3.9 16.8 - - + +
181A TRP* 3.8 32.8 - - + -
206A LEU* 4.9 1.1 - - + -
----------------------------------------------------------
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