Contacts of the strand formed by residues 3 - 16 (chain C) in PDB entry 3IEQ
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 3 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 4.5 3.6 - - + -
3A PHE* 4.0 21.1 - + + -
94A ARG* 4.2 10.0 - - - +
155A LEU* 3.2 27.0 - - + +
1B MET 3.5 12.8 - - - -
3B PHE* 4.0 21.1 - + + -
1C MET* 3.1 37.5 + - + -
2C ASP* 1.3 78.4 - - - +
4C ARG* 1.3 69.8 + - - +
94C ARG* 3.4 45.8 - - + -
155C LEU* 4.0 26.7 - - + -
156C VAL 3.3 15.5 - - - -
157C VAL* 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 4 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ASN* 3.2 27.6 - - - +
127A ASP* 3.2 34.8 + - - -
128A ARG* 3.5 30.5 - - - +
155A LEU* 4.1 0.7 - - - -
2C ASP* 2.8 39.4 + - - +
3C PHE* 1.3 87.4 - - - +
5C ILE* 1.3 63.8 + - - +
53C ALA* 3.2 26.8 + - - +
55C ALA* 5.3 1.0 - - - +
91C PHE* 3.7 35.6 - - + -
154C ALA 4.0 0.3 - - - +
155C LEU* 3.3 6.2 - - - +
156C VAL* 2.9 35.0 + - + +
158C ARG* 4.3 8.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 5 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ILE* 4.2 19.5 - - + -
6A GLY 4.5 0.9 - - - +
95A ASN* 2.9 37.0 + - - +
97A ASP* 3.8 5.9 - - - +
153A ALA* 3.6 17.5 - - + -
154A ALA 3.3 38.8 - - - +
155A LEU* 3.8 12.5 - - + +
5B ILE* 3.8 26.2 - - + -
4C ARG* 1.3 72.1 - - - +
6C GLY* 1.3 58.3 + - - +
53C ALA* 3.5 9.0 - - - -
154C ALA 3.4 4.5 - - - +
155C LEU* 3.6 24.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 6 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 3.4 11.2 - - - -
153A ALA* 4.9 3.2 - - - +
5B ILE* 4.5 1.2 - - - +
5C ILE* 1.3 75.6 - - - +
7C GLN* 1.3 60.4 + - - +
49C ALA* 3.3 24.2 - - - -
53C ALA* 3.5 5.2 - - - +
153C ALA* 3.4 5.7 - - - +
154C ALA 2.9 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 7 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ASP* 2.9 11.6 + - - +
98A SER* 3.2 12.0 - - - -
99A THR* 2.7 24.8 + - - -
132A LYS* 2.9 38.5 + - - -
151A GLN* 2.9 38.2 + - - +
152A ALA 4.4 2.7 - - - +
153A ALA* 3.9 31.4 - - + +
6C GLY* 1.3 75.4 - - - +
8C GLY* 1.3 64.1 + - - +
49C ALA* 3.6 5.7 - - - +
152C ALA 3.2 9.0 - - - +
153C ALA* 5.2 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 8 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 5.0 0.2 - - - -
132A LYS* 4.7 1.3 - - - -
7C GLN* 1.3 81.5 + - - +
9C TYR* 1.3 60.5 + - - +
45C ALA* 3.4 24.2 - - - -
48C ASP* 4.1 5.8 - - - -
49C ALA* 3.5 5.0 - - - +
151C GLN* 3.4 5.2 - - - +
152C ALA 2.8 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 9 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A THR* 4.9 5.9 + - + -
101A ILE* 3.8 21.3 - - + -
134A LYS* 3.2 43.6 - - + +
135A THR 5.0 1.6 - - - -
136A ASN* 2.5 32.4 + - - -
142A LEU* 5.1 2.1 - - + +
149A GLU* 5.2 4.2 + - - -
151A GLN* 3.3 37.5 - - - +
7C GLN* 4.7 0.4 - - - +
8C GLY* 1.3 71.9 - - - +
10C ASP* 1.3 67.2 + - - +
11C VAL* 3.6 19.3 - - + +
44C HIS 5.5 0.2 - - - +
45C ALA* 4.3 4.6 - - - +
48C ASP* 4.3 4.7 + - - +
141C TYR* 3.8 10.2 + - - -
149C GLU* 3.4 40.1 + - + -
150C ALA 3.5 6.1 - - - -
151C GLN* 5.0 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 10 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134A LYS* 3.2 18.9 + - - +
135A THR 5.7 0.2 - - - +
137A GLU* 5.2 1.7 - - - +
9C TYR* 1.3 82.5 - - - +
11C VAL* 1.3 77.4 + - - +
12C HIS* 2.9 11.0 + - - -
41C VAL* 3.5 21.0 - - + +
44C HIS* 3.1 12.7 - - + +
45C ALA 4.1 8.7 - - - +
149C GLU* 3.3 5.5 - - - +
150C ALA 2.9 32.1 + - - +
163C ZN 2.1 36.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 11 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A THR 5.0 1.6 - - - +
136A ASN* 3.4 48.9 - - - +
137A GLU* 3.0 23.8 - - + +
139A LEU* 3.7 19.5 - - + -
9C TYR* 3.6 11.8 - - + +
10C ASP* 1.3 81.4 + - - +
12C HIS* 1.3 72.0 + - - +
41C VAL* 3.7 0.7 - - - -
141C TYR* 4.1 15.0 - - + -
142C LEU* 4.4 0.4 - - + -
148C ILE 3.4 21.8 - - - +
149C GLU* 4.1 6.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 12 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 4.1 21.8 - - - -
139A LEU* 4.0 5.4 - - - -
10C ASP* 3.1 14.8 - - - -
11C VAL* 1.3 80.2 + - - +
13C GLN* 1.3 61.6 + - - +
33C LEU* 3.7 23.0 - - + +
34C LEU 2.8 24.3 + - - +
35C GLY* 4.2 7.4 - - - -
39C ALA* 3.8 25.3 - - + -
41C VAL* 3.9 9.0 - - + -
44C HIS* 3.3 6.2 + + - -
147C GLY* 3.1 3.3 - - - -
148C ILE 3.0 31.5 + - - +
163C ZN 2.1 32.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A GLU* 3.0 32.0 + - + +
138A LYS* 3.7 19.2 + - - +
139A LEU* 4.0 23.2 - - + +
12C HIS* 1.3 74.5 - - - +
14C LEU* 1.3 60.0 + - - +
15C VAL* 4.2 16.9 - - + +
32C GLY 3.6 0.2 - - - +
33C LEU* 3.3 5.2 - - - -
34C LEU* 2.9 46.5 + - + +
146C GLU* 3.5 9.4 - - - +
147C GLY* 4.2 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 1.3 72.2 - - - +
15C VAL* 1.3 63.9 + - - +
16C PRO* 4.8 0.2 - - - +
20C LEU* 4.0 8.7 - - + -
29C TYR* 4.4 22.7 - - + +
31C ARG* 3.8 23.6 + - + +
32C GLY* 3.4 18.4 - - - +
33C LEU* 3.6 24.0 - - + -
104C ALA 4.7 4.7 - - - +
145C GLY* 3.4 35.7 - - - +
146C GLU* 2.9 12.3 + - - +
147C GLY* 3.9 5.4 - - - +
148C ILE* 3.8 31.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C GLN* 4.2 15.0 - - + +
14C LEU* 1.3 79.0 - - - +
16C PRO* 1.4 77.1 - - + +
18C ARG* 3.8 22.7 - - + +
31C ARG* 3.3 7.2 - - - +
32C GLY 2.8 36.9 + - - +
34C LEU* 3.8 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C LEU 4.8 0.2 - - - +
15C VAL* 1.4 101.2 - - + +
17C GLY* 1.3 63.7 + - - +
18C ARG* 3.3 1.4 + - - +
30C GLU 4.2 4.7 - - - +
31C ARG* 4.0 18.2 - - + -
----------------------------------------------------------
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