Contacts of the helix formed by residues 102 - 116 (chain C) in PDB entry 3DC5
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 SER 102 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 3.5 15.1 - - - +
97C LYS* 4.2 11.3 - - - +
100C PHE* 3.2 4.6 + - - +
101C GLY* 1.3 78.2 - - - +
103C LEU* 1.3 64.4 + - - +
104C ASP* 3.6 8.7 + - - +
105C ASN* 2.9 32.1 + - - +
106C LEU* 3.2 16.1 + - - +
----------------------------------------------------------
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 PRO* 4.3 11.9 - - + -
93C MET* 4.0 37.3 - - + -
96C ILE* 3.7 17.7 - - + +
97C LYS* 5.4 0.6 - - - +
102C SER* 1.3 72.0 - - - +
104C ASP* 1.3 63.6 + - - +
106C LEU* 3.1 8.7 + - + -
107C GLN* 2.8 54.6 + - + +
182C TRP* 3.8 32.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 104 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C SER* 3.4 8.8 + - - +
103C LEU* 1.3 80.6 - - - +
105C ASN* 1.3 59.1 + - - +
107C GLN* 3.4 16.6 + - - +
108C LYS* 3.0 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100C PHE* 3.0 28.8 + - - +
101C GLY* 4.0 5.3 - - - -
102C SER* 2.9 25.8 + - - +
104C ASP* 1.3 75.7 - - - +
106C LEU* 1.3 58.8 + - - +
108C LYS* 3.3 5.6 + - - +
109C ARG* 2.9 43.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 106 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C ILE* 3.9 35.2 - - + -
100C PHE* 3.9 32.4 - - + +
102C SER 3.2 11.3 + - - +
103C LEU* 3.1 14.7 + - + +
105C ASN* 1.3 77.5 - - - +
107C GLN* 1.3 59.3 + - - +
109C ARG* 3.8 1.0 - - - +
110C LEU* 2.9 34.3 + - + +
125C LEU* 4.0 23.3 - - + -
136C ILE* 3.6 30.5 - - + -
177C TRP* 4.9 7.4 - - + -
182C TRP* 4.9 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C LEU* 2.8 43.9 + - + +
104C ASP* 3.7 21.6 - - - +
106C LEU* 1.3 72.5 - - - +
108C LYS* 1.3 55.4 + - - +
111C SER* 2.7 38.0 + - - -
177C TRP* 3.4 65.6 + - + +
182C TRP* 4.6 4.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ASP 3.0 17.1 + - - +
105C ASN* 3.7 5.6 - - - +
107C GLN* 1.3 77.1 - - - +
109C ARG* 1.3 60.4 + - + +
111C SER* 3.8 3.4 - - - -
112C ASP* 2.9 56.3 + - - +
174C HIS* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C ASP 4.5 3.8 + - - -
100C PHE* 3.6 43.2 + - + +
105C ASN* 2.9 29.8 + - - +
106C LEU* 3.9 2.7 - - - +
108C LYS* 1.3 78.5 - - + +
110C LEU* 1.3 60.6 + - - +
112C ASP* 3.8 5.7 - - - +
113C ILE* 3.2 30.0 + - + +
136C ILE* 3.7 20.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106C LEU* 2.9 21.1 + - + +
109C ARG* 1.3 70.6 - - - +
111C SER* 1.3 67.3 + - - +
112C ASP 3.2 0.2 + - - -
113C ILE* 3.3 14.8 + - + +
114C THR* 2.8 41.3 + - - +
123C GLY 4.0 0.4 - - - -
124C TRP* 3.7 29.6 - - - +
125C LEU* 4.1 26.9 - - + +
136C ILE* 3.7 15.8 - - + +
152C PHE* 4.4 6.3 - - + +
154C ILE* 4.2 9.9 - - + -
177C TRP* 3.8 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107C GLN* 2.7 28.5 + - - +
108C LYS* 3.8 4.5 - - - -
110C LEU* 1.3 73.9 - - - +
112C ASP* 1.3 57.5 + - - +
114C THR* 3.3 0.9 + - - -
115C ILE* 2.8 37.2 + - - +
154C ILE* 5.2 0.2 - - - -
173C VAL* 3.7 19.1 - - - +
174C HIS* 3.9 25.0 - - - -
177C TRP* 2.8 27.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 112 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C LYS* 2.9 48.1 + - - +
109C ARG* 3.8 6.4 - - - +
110C LEU 3.2 0.4 - - - -
111C SER* 1.3 79.3 - - - +
113C ILE* 1.3 64.7 + - + +
115C ILE* 3.4 9.0 + - - +
116C ALA* 3.1 23.6 + - - +
174C HIS* 4.8 8.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C ARG 3.2 14.1 + - - +
110C LEU* 3.5 14.4 - - + +
112C ASP* 1.3 81.7 - - + +
114C THR* 1.3 65.0 + - - +
116C ALA* 3.3 15.5 + - - +
117C VAL* 3.4 9.2 + - - +
136C ILE* 3.9 22.2 - - + +
137C ALA* 3.7 42.2 - - - +
138C THR* 3.5 18.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C LEU* 2.8 30.1 + - - +
111C SER 3.6 3.8 - - - -
113C ILE* 1.3 75.7 - - - +
115C ILE* 1.3 65.5 + - - +
117C VAL* 3.2 24.5 + - - +
123C GLY* 3.3 20.1 - - - -
138C THR* 4.3 2.0 - - - -
154C ILE* 3.8 27.5 - - + +
156C VAL* 3.5 32.8 - - + +
169C ARG* 3.7 4.3 + - - -
173C VAL* 4.2 7.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C SER 2.8 24.1 + - - +
112C ASP* 3.8 10.3 - - - +
113C ILE 3.4 0.2 - - - -
114C THR* 1.3 76.5 - - - +
116C ALA* 1.3 57.2 + - + +
117C VAL 3.3 0.4 - - - +
169C ARG* 2.9 30.1 + - - +
170C PRO* 3.7 41.1 - - + -
173C VAL* 3.7 23.3 - - + -
174C HIS* 3.8 27.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C ASP 3.1 16.4 + - - +
113C ILE* 3.6 10.5 - - - +
114C THR 3.2 0.6 - - - -
115C ILE* 1.3 76.2 - - + +
117C VAL* 1.3 65.3 + - - +
118C GLN* 3.2 14.0 + - - +
----------------------------------------------------------
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