Contacts of the helix formed by residues 95 - 108 (chain C) in PDB entry 2W4T
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 ASN 95 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 4.7 0.2 - - - -
75C GLN* 3.4 36.2 - - - +
76C SER* 3.5 10.8 + - - +
93C TYR* 3.4 20.9 - - + +
94C LEU* 1.3 74.8 - - - +
96C GLU* 1.3 54.3 + - - +
97C ALA* 2.5 45.5 + - - +
98C SER* 2.6 42.7 + - - -
99C VAL* 3.0 7.6 + - - -
697C LEU* 4.0 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C PHE* 3.7 26.5 - - + -
75C GLN* 6.1 0.2 - - - -
95C ASN* 1.3 70.0 - - - +
97C ALA* 1.3 56.4 + - - +
99C VAL* 3.2 16.6 - - - +
100C LEU* 3.3 18.2 - - - +
688C LEU* 3.2 32.0 - - + +
691C LEU* 3.5 27.2 - - - +
692C GLN* 3.4 22.8 - - + +
696C VAL* 4.0 7.1 - - - +
697C LEU* 4.5 15.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 2.8 49.4 - - + -
43C PHE* 3.2 40.1 - - + -
75C GLN* 4.6 0.2 - - + -
95C ASN* 2.5 25.7 + - - +
96C GLU* 1.3 74.3 - - - +
98C SER* 1.3 56.7 + - - +
99C VAL 3.4 0.4 - - - -
100C LEU* 4.6 0.9 - - - -
101C TYR* 3.2 9.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 98 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 4.2 11.0 - - - -
76C SER 5.0 0.2 - - - -
78C ASN* 2.9 31.1 + - - +
93C TYR 2.6 18.6 + - - -
94C LEU* 3.4 3.5 - - - +
95C ASN* 2.6 38.1 + - - -
97C ALA* 1.3 72.8 - - - +
99C VAL* 1.3 67.9 + - - +
101C TYR* 3.4 2.4 + - - +
102C ASN* 2.9 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 99 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 3.3 16.5 - - + +
94C LEU* 3.7 32.3 - - + +
95C ASN 3.3 15.3 - - - +
96C GLU* 3.2 28.5 - - - +
98C SER* 1.3 79.6 + - - +
100C LEU* 1.3 79.8 + - - +
102C ASN* 3.0 13.3 + - - +
103C LEU* 3.0 15.0 + - + +
691C LEU* 2.9 28.5 - - + -
696C VAL* 5.1 3.1 - - + -
697C LEU* 5.0 11.2 - - - -
700C ILE* 5.9 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 6.0 0.7 - - + -
41C GLU* 5.1 8.3 - - - +
43C PHE* 4.7 4.9 - - + -
96C GLU 3.3 15.0 + - - +
97C ALA* 4.4 3.1 - - - +
99C VAL* 1.3 81.9 - - - +
101C TYR* 1.3 62.9 + - - +
103C LEU* 4.7 6.1 - - + -
104C ARG* 3.2 30.2 + - + +
684C ALA* 3.5 7.9 - - + +
687C VAL* 3.2 29.6 - - + -
688C LEU* 2.3 59.7 - - + +
691C LEU* 3.4 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 101 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C TRP* 2.8 45.7 - + + -
41C GLU* 5.9 1.3 - - - -
77C MET* 5.6 12.7 - - + +
83C GLU* 5.4 15.3 - - + +
97C ALA 3.2 5.2 + - - +
98C SER 3.6 3.8 - - - +
99C VAL 3.0 0.8 + - - -
100C LEU* 1.3 80.7 - - - +
102C ASN* 1.3 66.5 + - - +
104C ARG* 3.8 3.3 - - + +
105C SER* 2.2 57.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 102 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C ASN* 4.4 0.9 + - - +
82C PHE 3.3 13.1 + - - -
84C LYS* 4.3 4.8 - - - +
85C LEU* 3.4 10.7 - - + +
88C MET* 2.8 40.3 - - + +
91C MET* 2.8 38.7 - - - +
98C SER* 2.9 16.2 + - - +
99C VAL 3.0 0.8 + - - -
101C TYR* 1.3 84.0 - - - +
103C LEU* 1.3 69.7 + - - +
105C SER* 3.1 6.4 + - - -
106C ARG* 3.0 26.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C MET* 5.6 3.1 - - + -
99C VAL 3.0 12.5 + - - +
100C LEU* 4.0 8.7 - - + +
102C ASN* 1.3 77.5 - - + +
104C ARG* 1.3 54.8 + - - +
105C SER 2.7 1.2 + - - -
106C ARG* 2.7 30.0 + - + +
107C TYR* 2.8 14.9 + - - -
111C LEU 6.1 0.7 - - - +
112C ILE 6.0 0.7 - - - -
114C THR* 3.7 19.1 - - + +
121C ILE* 2.9 42.6 - - + -
123C VAL* 4.1 17.0 - - + -
669C ARG* 4.0 17.5 - - - +
671C ILE* 5.2 2.9 - - + -
691C LEU* 4.5 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C GLU* 2.5 25.1 + - - +
100C LEU* 3.2 18.9 + - + +
101C TYR* 4.0 4.0 - - + +
103C LEU* 1.3 78.7 - - - +
105C SER* 1.3 61.4 + - - +
107C TYR* 4.1 8.3 - - - +
108C THR* 3.0 33.3 + - + +
682C VAL* 2.4 73.0 + - + +
684C ALA* 2.3 49.0 - - - +
687C VAL* 5.5 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLU* 4.0 6.5 - - - -
84C LYS* 3.9 20.2 - - - +
101C TYR* 2.2 53.6 + - - -
102C ASN* 3.2 8.5 - - - -
103C LEU 2.7 4.9 + - - -
104C ARG* 1.3 70.5 - - - +
106C ARG* 1.3 65.3 + - - +
108C THR* 3.1 17.6 + - - -
109C SER* 3.2 10.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C VAL* 4.0 0.8 - - - +
84C LYS* 2.6 44.0 + - + -
85C LEU* 2.6 35.1 + - - -
86C GLU* 2.2 43.0 + - - -
102C ASN 3.1 19.3 - - - +
103C LEU* 2.7 11.4 + - + +
105C SER* 1.3 68.6 - - - +
107C TYR* 1.3 55.1 + - - +
109C SER* 2.6 35.5 + - - -
110C GLY 3.4 3.5 + - - -
111C LEU* 3.2 33.7 + - + +
113C TYR 2.6 24.7 + - - -
114C THR* 2.3 27.9 + - - +
150C PRO* 3.6 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 2.8 18.9 + - - +
104C ARG* 4.0 9.0 - - - +
106C ARG* 1.3 72.5 - - - +
108C THR* 1.3 60.5 + - + +
109C SER 2.6 12.1 + - - -
110C GLY* 2.9 13.5 + - - -
111C LEU 3.0 12.4 + - - +
112C ILE* 4.8 5.3 - - + +
123C VAL* 3.2 35.9 - - + -
124C ASN* 3.5 28.8 + - - -
125C PRO* 4.0 7.8 + - + -
671C ILE* 6.2 0.2 - - + -
673C PRO* 4.4 10.4 - - + +
679C PRO* 3.8 0.7 - - - +
680C GLY* 2.7 54.4 + - - -
681C LEU 3.7 3.2 + - - -
682C VAL* 3.6 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ARG* 3.0 25.3 + - + +
105C SER* 3.1 14.6 + - - -
107C TYR* 1.3 87.1 - - + +
109C SER* 1.3 59.2 + - - +
110C GLY 3.7 0.4 - - - -
680C GLY 5.1 4.9 - - - +
682C VAL* 4.5 8.3 - - + -
----------------------------------------------------------
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