Contacts of the helix formed by residues 14 - 25 (chain G) in PDB entry 3O65
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 LEU 14 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLN* 4.1 2.4 - - - +
11G GLU 4.0 15.0 + - - +
12G GLY* 3.4 4.4 + - - -
13G PHE* 1.3 78.2 - - - +
15G CYS* 1.3 62.5 + - - +
16G ALA 3.4 2.5 - - - -
17G GLN* 3.3 26.4 + - + +
18G HIS* 2.9 41.4 + - + +
31G PRO* 4.7 19.7 - - + -
34G LEU* 6.4 0.2 - - + -
74G GLY* 5.0 8.3 - - - +
76G PHE* 5.4 14.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 15 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G GLN* 3.1 23.0 + - - +
13G PHE 3.1 6.0 + - - -
14G LEU* 1.3 74.7 - - - +
16G ALA* 1.3 65.2 + - - +
18G HIS* 3.0 4.5 + - - +
19G CYS* 2.7 37.3 + - - +
74G GLY 5.5 0.4 + - - -
120G HIS* 3.7 3.6 - - + -
121G TRP* 3.5 28.2 - - - +
136G SER* 4.4 1.1 + - - -
75H GLY 3.4 7.6 - - - -
76H NEH 1.8 54.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU 3.4 0.8 + - - -
15G CYS* 1.3 82.3 - - - +
17G GLN* 1.3 63.1 + - - +
19G CYS* 3.6 5.3 - - - +
20G LEU* 3.1 29.0 + - - +
34G LEU* 4.4 6.3 - - + -
76G PHE* 3.8 35.9 - - + -
80G VAL* 6.2 0.2 - - + -
81G ILE* 4.0 13.2 - - + +
121G TRP* 3.7 24.5 - - + -
75H GLY 4.7 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLU* 3.4 19.0 + - - -
14G LEU* 3.3 23.0 + - + +
15G CYS 3.1 0.8 - - - -
16G ALA* 1.3 75.9 - - - +
18G HIS* 1.3 80.6 + - - +
20G LEU* 3.1 7.7 + - - +
21G ASN* 2.9 25.7 + - - +
29G PHE* 3.5 30.3 + - - +
31G PRO* 3.5 32.1 - - - +
34G LEU* 3.6 22.6 - - + +
76G PHE* 5.4 0.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 18 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G GLU* 3.1 37.9 + - + +
9G LYS 3.7 13.2 - - - -
10G GLN* 3.3 34.9 - - + +
11G GLU 4.1 5.5 + - - -
14G LEU* 2.9 41.8 + - + +
15G CYS 3.0 2.8 + - - +
17G GLN* 1.3 88.1 + - - +
19G CYS* 1.3 64.8 + - - +
21G ASN* 3.1 1.6 + - - +
22G ASN* 2.8 31.1 + - - +
136G SER* 3.5 22.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 19 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G CYS 2.7 21.1 + - - +
16G ALA* 3.6 5.6 - - - +
18G HIS* 1.3 74.9 - - - +
20G LEU* 1.3 65.3 + - - +
22G ASN* 3.4 3.5 + - - +
23G LEU* 3.2 8.7 + - - +
81G ILE* 5.3 4.0 - - + -
114G ILE* 3.8 22.0 - - - -
121G TRP* 3.9 14.6 - - + +
122G PHE* 3.5 32.1 - - - +
123G THR* 2.8 43.6 + - - +
136G SER* 5.1 1.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 20 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ALA 3.1 11.3 + - - +
17G GLN 3.1 8.6 + - - +
19G CYS* 1.3 82.2 - - - +
21G ASN* 1.3 63.1 + - - +
23G LEU* 3.2 5.0 + - + +
24G LEU* 3.0 27.0 + - + +
29G PHE* 3.6 28.5 - - + -
34G LEU* 3.9 17.9 - - + -
81G ILE* 4.3 23.1 - - + +
84G ALA* 3.5 28.3 - - + -
85G LEU* 3.8 35.9 - - + -
114G ILE* 4.8 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 21 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G PHE* 3.5 8.2 - - + -
8G GLU* 2.9 31.1 + - - +
17G GLN* 2.9 23.3 + - - +
18G HIS 3.7 2.7 - - - +
20G LEU* 1.3 71.3 - - - +
22G ASN* 1.3 53.6 + - - +
24G LEU* 3.5 3.3 - - - +
25G GLN* 2.6 31.9 + - - -
26G GLY 3.1 26.1 + - - +
27G GLU* 4.1 3.8 - - - +
28G TYR* 3.2 7.1 + - - +
29G PHE* 2.7 50.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 22 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G PHE* 3.4 14.9 - - - +
7G HIS* 4.3 2.1 + - - -
8G GLU* 2.8 44.9 + - - +
18G HIS* 2.8 31.6 + - - +
19G CYS* 3.8 5.1 - - - +
21G ASN* 1.3 68.5 - - - +
23G LEU* 1.3 67.2 + - - +
25G GLN* 2.9 25.3 + - - +
123G THR* 4.5 2.7 - - - -
125G ARG* 4.6 0.5 - - - -
134G LEU* 3.0 47.5 + - + +
136G SER* 4.3 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 23 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19G CYS 3.2 3.2 + - - +
20G LEU* 3.2 8.6 + - + +
22G ASN* 1.3 80.2 - - - +
24G LEU* 1.3 61.1 + - + +
85G LEU* 3.7 30.7 - - + -
90G LEU* 4.9 0.7 - - + -
112G SER* 3.6 32.5 - - - +
114G ILE* 3.9 20.9 - - + -
123G THR* 3.6 25.4 - - + +
125G ARG* 2.7 38.1 + - - +
166G VAL* 4.1 13.5 - - + -
170G LEU* 3.8 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20G LEU* 3.0 17.5 + - - +
21G ASN 3.9 1.1 - - - +
23G LEU* 1.3 98.1 - - + +
25G GLN* 1.3 71.2 + - - +
26G GLY 3.4 0.2 - - - -
28G TYR* 3.6 41.1 + - + -
29G PHE* 3.7 30.7 - - + -
85G LEU* 4.2 13.7 - - + -
88G TRP* 3.9 19.1 - - + -
90G LEU* 4.3 10.3 - - + -
125G ARG* 4.2 1.2 + - - -
170G LEU* 5.3 0.2 - - + -
171G PRO* 3.9 29.7 - - + +
173G CYS* 5.1 2.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E VAL* 5.2 2.6 - - - +
4G PHE 4.3 1.4 - - - +
5G ILE* 3.7 5.2 - - - +
6G PHE* 2.8 64.5 + - - +
21G ASN 2.6 14.6 + - - -
22G ASN 2.9 18.5 + - - +
23G LEU 3.2 2.6 - - - -
24G LEU* 1.3 77.7 - - - +
26G GLY* 1.3 55.0 + - - +
28G TYR* 4.1 2.5 + - - -
125G ARG* 3.5 15.7 - - - +
127G PHE* 3.7 21.7 - - + -
134G LEU* 4.2 3.4 - - - +
173G CYS* 3.4 39.0 - - + -
174G GLU* 4.8 14.1 + - - +
----------------------------------------------------------
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