Contacts of the helix formed by residues 5 - 21 (chain C) in PDB entry 4U2M
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 GLN 5 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE 3.1 1.0 + - - -
4C PRO* 1.3 91.8 - - + +
6C HIS* 1.3 64.1 + - - +
7C SER 3.3 2.5 - - - -
8C GLN* 3.2 15.3 + - + +
9C HIS* 3.0 22.5 + - - +
196D ASN 4.7 4.7 + - - +
197D LEU* 4.2 3.4 - - - +
198D ASP* 3.5 50.4 + - + +
199D PRO* 3.9 10.5 - - + +
234D TYR* 4.0 9.3 + - - -
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Residues in contact with HIS 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.1 27.0 + - + +
4C PRO 3.4 0.4 - - - -
5C GLN* 1.3 79.1 - - - +
7C SER* 1.3 56.5 + - - +
9C HIS* 3.1 3.4 + + - +
10C VAL* 3.0 44.5 + - + +
142C LEU* 3.8 7.4 - - + -
176C CYS* 3.8 14.4 - - - -
212C PHE* 3.6 20.0 + + - -
213C MET* 2.8 28.9 + - - -
216C SER* 3.2 28.7 - - - +
200D GLU* 2.6 41.8 + - - +
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Residues in contact with SER 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE 4.8 0.2 + - - -
4C PRO 4.8 7.0 + - - -
5C GLN 3.3 0.2 - - - -
6C HIS* 1.3 78.6 - - - +
8C GLN* 1.3 63.4 + - - +
10C VAL* 3.5 4.6 + - - +
11C LEU* 3.1 19.1 + - - +
138C ALA* 3.6 30.1 - - - +
139C SER* 3.0 28.8 + - - -
142C LEU* 3.9 25.5 - - - +
216C SER* 4.0 5.5 + - - -
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Residues in contact with GLN 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C PRO 5.7 0.2 - - - +
5C GLN* 3.2 16.0 + - + +
6C HIS 3.2 0.2 - - - -
7C SER* 1.3 80.0 + - - +
9C HIS* 1.3 62.8 + - - +
11C LEU* 3.4 11.3 + - - +
12C GLU* 3.0 56.9 + - - +
79C THR 5.5 3.6 + - - -
138C ALA* 3.6 20.2 - - + +
198D ASP* 6.1 0.2 - - - +
234D TYR* 5.9 3.6 - - + -
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Residues in contact with HIS 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLN 3.0 10.3 + - - +
6C HIS* 3.4 9.2 - + - +
8C GLN* 1.3 77.4 - - - +
10C VAL* 1.3 66.7 + - + +
12C GLU* 3.4 13.0 + - - +
13C GLN* 3.0 57.6 + - + +
175C ALA 4.1 10.1 + - - -
176C CYS* 5.7 0.4 - - - -
198D ASP* 3.1 28.9 + - - +
200D GLU* 3.5 55.9 + - + +
201D ILE* 4.4 9.9 - - + +
230D ALA* 6.2 0.7 - - + -
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Residues in contact with VAL 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C HIS* 3.0 48.6 + - + +
7C SER* 3.7 6.7 - - - +
8C GLN 3.3 0.2 - - - -
9C HIS* 1.3 78.6 - - + +
11C LEU* 1.3 57.9 + - - +
13C GLN* 3.1 9.7 + - - +
14C LEU* 2.9 45.8 + - + +
141C VAL* 6.3 0.7 - - + -
142C LEU* 4.1 23.1 - - + -
145C LEU* 5.1 3.8 - - + -
172C VAL* 5.3 5.2 - - + -
175C ALA* 4.4 10.1 - - + -
176C CYS* 3.9 14.8 - - - -
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER 3.1 17.6 + - - +
8C GLN* 3.7 12.8 - - - +
9C HIS 3.3 0.2 - - - -
10C VAL* 1.3 76.9 - - - +
12C GLU* 1.3 63.3 + - - +
14C LEU* 3.2 13.2 + - + +
15C ASN* 2.9 23.0 + - - +
41C VAL* 5.8 1.1 - - + -
77C MET 3.5 20.6 - - - +
78C TYR* 3.4 22.7 - - + +
79C THR* 4.0 20.6 - - - +
80C ALA* 4.4 3.6 - - + -
137C HIS* 4.2 10.1 - - + -
138C ALA* 3.9 21.3 - - + -
141C VAL* 4.4 25.8 - - + -
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Residues in contact with GLU 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C GLN* 3.0 49.4 + - - +
9C HIS* 3.7 18.0 + - - +
10C VAL 3.4 0.2 - - - -
11C LEU* 1.3 76.7 - - + +
13C GLN* 1.3 61.8 + - - +
15C ASN* 3.3 7.5 + - - +
16C GLN* 2.9 28.6 + - - +
198D ASP* 4.6 1.2 - - - +
201D ILE* 5.1 1.2 - - - +
230D ALA 5.3 1.9 - - - +
233D MET* 3.8 16.5 - - + +
234D TYR* 3.6 44.2 - - - +
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Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C HIS* 3.0 42.1 + - + +
10C VAL 3.1 7.2 + - - +
12C GLU* 1.3 76.2 - - - +
14C LEU* 1.3 61.9 + - - +
16C GLN* 3.3 16.9 + - - +
17C GLN* 2.9 34.6 + - - +
174C MET 4.7 3.6 + - - -
175C ALA* 3.4 42.2 + - + +
230D ALA* 3.7 23.6 - - - +
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Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C VAL* 2.9 34.6 + - + +
11C LEU* 3.2 15.7 + - + +
13C GLN* 1.3 75.3 - - - +
15C ASN* 1.3 59.5 + - - +
17C GLN* 3.3 8.0 + - - +
18C ARG 3.0 22.2 + - - -
38C HIS* 3.7 0.9 - - - -
41C VAL* 3.9 20.4 - - + -
78C TYR* 3.5 24.1 - - + -
141C VAL* 4.6 10.1 - - + -
145C LEU* 4.3 13.7 - - + -
171C THR* 2.9 47.3 - - + +
172C VAL* 4.7 4.5 - - + +
175C ALA* 4.5 4.5 - - + -
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Residues in contact with ASN 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C LEU 2.9 11.2 + - - +
12C GLU* 3.6 7.4 - - - +
14C LEU* 1.3 74.6 - - - +
16C GLN* 1.3 65.3 + - - +
18C ARG* 3.0 32.6 + - - +
19C GLN* 3.0 43.8 + - - +
75C GLU* 5.2 1.0 + - - -
78C TYR* 3.5 30.4 - - - +
79C THR* 3.7 18.7 - - - +
233D MET* 3.9 9.1 - - - +
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Residues in contact with GLN 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLU 2.9 15.0 + - - +
13C GLN* 3.6 23.5 + - - +
15C ASN* 1.3 76.8 - - - +
17C GLN* 1.3 62.7 + - + +
19C GLN* 3.3 5.2 + - - +
20C LEU* 3.1 31.6 + - + +
226D MET* 2.9 48.4 + - + +
229D MET* 3.6 27.1 - - + +
230D ALA* 3.6 21.6 - - + +
233D MET* 3.9 21.4 - - - +
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 2.9 21.0 + - - +
14C LEU* 3.5 8.6 - - - +
15C ASN 3.3 0.2 - - - -
16C GLN* 1.3 74.5 - - + +
18C ARG* 1.3 60.2 + - - +
20C LEU 3.1 2.8 + - - -
21C GLY 2.9 24.4 + - - -
22C LEU* 2.9 36.9 + - + +
23C LEU* 4.0 2.6 - - - +
38C HIS* 3.1 8.5 + - - +
171C THR* 2.9 52.6 + - - +
174C MET* 3.7 27.2 - - + +
175C ALA* 3.7 19.4 - - - +
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Residues in contact with ARG 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 3.6 27.9 + - - +
188A LEU* 4.6 18.9 - - - +
14C LEU 3.0 13.8 + - - +
15C ASN* 3.0 29.5 + - - +
17C GLN* 1.3 76.8 - - - +
19C GLN* 1.3 63.8 + - - +
21C GLY* 3.1 12.1 + - - -
24C CYS* 3.8 12.2 - - - -
35C PHE* 5.5 2.8 - - - -
36C LYS* 3.4 26.3 - - - +
38C HIS* 3.9 2.2 - - + -
71C GLY 5.3 0.8 + - - -
74C LEU* 4.1 24.4 - - - +
75C GLU* 3.0 34.6 + - - +
78C TYR* 3.6 42.2 - - + +
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Residues in contact with GLN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A GLN* 4.8 3.0 + - - +
188A LEU* 3.8 40.4 - - + +
15C ASN* 3.0 46.6 + - - +
16C GLN 3.3 4.7 + - - +
18C ARG* 1.3 79.7 - - - +
20C LEU* 1.3 62.5 + - - +
21C GLY 3.7 0.3 + - - -
75C GLU* 6.0 0.4 + - - -
229D MET* 3.4 15.4 - - + +
233D MET* 4.1 10.9 - - - +
241D VAL* 4.4 2.1 - - - +
245D ARG* 2.2 42.7 + - - +
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Residues in contact with LEU 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C GLN* 3.1 22.1 + - + +
17C GLN 3.1 4.9 + - - +
19C GLN* 1.3 78.9 - - - +
21C GLY* 1.3 60.5 + - - +
22C LEU* 3.4 20.4 + - + +
226D MET* 3.5 40.6 - - + -
229D MET* 4.1 15.9 - - + -
245D ARG* 4.2 10.1 - - + -
248D ILE* 3.8 35.2 - - + -
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN 2.9 5.4 + - - -
18C ARG 3.1 11.4 + - - -
19C GLN 3.4 1.0 + - - -
20C LEU* 1.3 76.3 - - - +
22C LEU* 1.3 63.7 + - - +
23C LEU 3.4 2.1 + - - -
24C CYS* 3.5 22.2 + - - +
36C LYS* 5.0 9.4 - - - -
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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) + - + + + + + -
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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