Contacts of the strand formed by residues 1 - 15 (chain C) in PDB entry 1H48
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 MET 1 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 3.9 31.9 - - + +
92A GLY* 5.4 5.7 - - - -
93A ASN* 4.3 1.2 - - - +
153A LEU* 3.5 18.1 - - + +
155A ILE* 6.1 1.0 - - - +
-1B LEU 5.7 1.6 - - - +
1B MET* 3.8 38.6 - - + +
-1C LEU* 5.2 9.9 - - + -
0C GLU* 1.3 82.1 - - - +
2C ARG* 1.3 68.5 + - - +
92C GLY* 5.1 1.3 - - - -
153C LEU* 3.6 35.2 - - + -
154C LEU 3.1 4.5 - - - +
155C ILE* 3.7 30.3 - - + -
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Residues in contact with ARG 2 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A GLY 4.8 1.1 + - - +
93A ASN* 3.4 25.9 - - + +
94A VAL 5.4 0.4 + - - -
125A ASP* 2.7 25.7 + - - +
126A ASP* 3.0 34.8 + - - +
153A LEU* 4.1 0.9 - - - -
0C GLU* 3.5 22.3 + - - +
1C MET* 1.3 80.7 - - - +
3C ILE* 1.3 61.1 + - - +
50C GLY 5.0 0.6 + - - -
51C ALA* 2.6 33.7 + - - +
52C ALA 5.1 0.2 - - - -
53C ALA* 3.6 14.8 - - - +
89C TYR* 3.1 37.7 + - + -
152C ALA 3.6 1.0 - - - +
153C LEU* 3.3 10.1 - - - +
154C LEU* 2.7 46.6 + - + +
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Residues in contact with ILE 3 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 3.7 28.3 - - + -
4A GLY 4.7 0.9 - - - +
93A ASN* 2.8 41.4 + - - +
94A VAL* 5.3 0.2 - - - -
95A ASP* 4.1 4.7 - - - +
151A VAL* 3.7 36.8 - - + +
152A ALA 4.0 5.2 - - - +
153A LEU* 3.7 25.0 - - + +
3B ILE* 3.3 35.0 - - + -
151B VAL* 6.0 1.8 - - + -
2C ARG* 1.3 73.7 - - - +
4C GLY* 1.3 61.3 + - - +
51C ALA* 3.3 8.7 - - - -
152C ALA 3.4 3.1 - - - -
153C LEU* 4.1 5.6 - - + -
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Residues in contact with GLY 4 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ASP* 3.5 9.6 - - - -
151A VAL* 4.0 4.5 - - - -
3C ILE* 1.3 76.0 - - - +
5C HIS* 1.3 61.5 + - - +
47C ALA* 3.2 24.5 - - - -
51C ALA* 3.6 4.1 - - - +
151C VAL* 3.2 8.5 - - - +
152C ALA 3.0 30.1 + - - -
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Residues in contact with HIS 5 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A HIS* 4.9 4.0 - + - -
95A ASP* 2.8 10.1 + - - +
97A THR* 3.4 14.9 + - - +
130A LYS* 2.7 35.9 + - - +
149A GLU* 3.4 36.0 - - + +
150A ALA* 5.5 0.4 - - - -
151A VAL* 3.8 30.1 - - + +
204A MN 3.1 7.2 + - - -
5B HIS* 5.0 2.7 - - - -
4C GLY* 1.3 73.8 - - - +
6C GLY* 1.3 71.4 + - - +
7C PHE* 4.0 5.6 - - + -
47C ALA* 3.7 6.2 - - - +
149C GLU* 2.6 25.5 + - + -
150C ALA 3.3 16.4 - - - -
151C VAL* 4.2 12.6 - - + -
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Residues in contact with GLY 6 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97A THR* 4.7 0.2 - - - -
130A LYS* 4.4 2.0 - - - -
5C HIS* 1.3 84.3 - - - +
7C PHE* 1.3 62.2 + - - +
43C ALA* 3.4 24.2 - - - -
46C ASP* 3.9 7.6 - - - -
47C ALA* 3.7 5.2 - - - +
149C GLU* 3.2 4.2 - - - -
150C ALA 2.9 29.9 + - - -
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Residues in contact with PHE 7 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A THR* 4.3 13.4 - - + +
99A ILE* 3.7 26.9 - - + -
132A THR* 3.5 24.3 + - + +
134A THR* 4.2 11.9 - - + -
149A GLU* 4.1 1.3 - - - +
5C HIS* 4.0 13.0 + - + -
6C GLY* 1.3 75.6 - - - +
8C ASP* 1.3 66.2 + - - +
9C VAL* 3.6 31.6 - - + -
43C ALA* 4.0 3.6 - - - +
46C ASP* 4.5 8.8 - - - +
99C ILE* 5.0 0.4 - - + -
147C ALA* 4.3 17.3 - - + -
148C CYS 3.2 15.0 - - - -
149C GLU* 3.8 20.9 - - + -
904C GPP 3.5 45.5 - - + -
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Residues in contact with ASP 8 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A THR* 3.5 15.6 + - - -
133A THR 4.5 0.9 - - - +
135A GLU* 5.5 0.2 - - - +
203A C5P 4.0 1.0 + - - -
7C PHE* 1.3 82.3 - - - +
9C VAL* 1.3 83.3 + - - +
10C HIS* 3.2 6.3 + - - -
39C VAL* 3.6 21.5 - - + +
42C HIS* 3.1 12.6 + - - +
43C ALA* 4.1 8.7 - - + +
46C ASP* 6.0 0.7 - - - +
57C ILE* 5.6 0.7 - - - -
147C ALA* 3.3 0.9 - - - +
148C CYS 2.9 31.7 + - - +
902C CDI 3.4 7.0 + - - -
903C ZN 2.1 37.2 - - - -
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Residues in contact with VAL 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A THR 4.5 3.4 + - - +
134A THR* 3.7 35.4 - - + +
135A GLU* 3.2 17.8 - - - +
137A LEU* 4.1 3.1 - - + -
7C PHE* 3.6 24.9 - - + -
8C ASP* 1.3 88.8 + - - +
10C HIS* 1.3 82.2 + - - +
39C VAL* 3.7 0.2 - - - -
139C PHE* 3.6 40.2 - - + -
146C ILE 3.3 8.7 - - - +
147C ALA* 3.9 4.7 - - + -
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Residues in contact with HIS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 4.2 10.0 - - - +
8C ASP* 3.4 8.7 - - - -
9C VAL* 1.3 79.8 + - - +
11C ALA* 1.3 60.5 + - - +
31C LEU* 3.7 19.3 - - + +
32C LEU 3.2 20.7 + - - +
33C ALA* 4.0 9.2 - - + -
37C GLY* 3.7 23.1 - - - +
39C VAL* 3.7 9.1 - - + +
42C HIS* 3.3 4.8 + - - -
145C GLY* 3.1 2.6 - - - -
146C ILE 2.9 33.4 + - - -
902C CDI 3.1 32.0 + - - -
903C ZN 2.1 36.7 - - - -
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Residues in contact with ALA 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A GLU* 4.4 15.5 - - + +
137A LEU* 3.9 25.3 - - + +
10C HIS* 1.3 74.2 - - - +
12C PHE* 1.3 62.8 + - - +
31C LEU* 3.4 5.7 - - - -
32C LEU* 2.8 46.3 + - + +
144C GLU 3.7 7.6 - - - +
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Residues in contact with PHE 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 1.3 77.9 - - - +
13C GLY* 1.3 57.8 + - - +
18C ILE* 4.4 3.6 - - + -
27C TYR* 3.6 26.0 - + - -
29C LYS* 3.5 29.2 - - + -
30C GLY 3.2 15.3 - - - +
31C LEU* 3.6 12.8 - - + -
32C LEU* 3.8 10.7 - - - +
102C ALA 3.6 17.0 - - - -
103C PRO* 4.8 0.2 - - + -
143C GLY* 3.1 31.0 - - - +
144C GLU 3.0 22.0 + - - +
145C GLY* 3.6 16.6 - - - -
146C ILE* 3.4 35.4 - - + -
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Residues in contact with GLY 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA 3.9 0.4 + - - -
12C PHE* 1.3 76.5 - - - +
14C GLY* 1.3 67.4 + - - -
29C LYS* 4.2 5.8 - - - +
30C GLY* 2.9 22.9 + - - -
31C LEU 3.8 2.3 + - - -
32C LEU* 3.9 23.5 - - - +
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Residues in contact with GLY 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C GLY* 1.3 76.7 - - - -
15C GLU* 1.3 68.6 + - - +
28C GLU 4.2 1.2 - - - +
29C LYS* 3.4 10.4 - - - +
30C GLY 3.1 8.5 + - - -
32C LEU* 4.5 4.4 - - - +
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Residues in contact with GLU 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C GLY* 1.3 75.0 - - - +
16C GLY* 1.3 71.7 + - - +
17C PRO 4.0 1.9 - - - +
28C GLU 4.4 8.0 - - - +
30C GLY* 3.2 16.6 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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