Contacts of the strand formed by residues 15 - 24 (chain C) in PDB entry 1MF8
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 GLU 15 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C ALA* 4.1 0.2 - - - -
12C VAL* 2.7 43.2 + - + +
13C ASP* 3.4 3.9 - - + +
14C GLY* 1.3 74.5 - - - +
16C PRO* 1.3 81.0 - - - +
17C LEU* 4.4 1.4 - - + +
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Residues in contact with PRO 16 (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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10C ILE 3.8 7.9 - - - +
11C ALA* 4.1 5.2 - - + -
14C GLY 3.2 7.8 - - - +
15C GLU* 1.3 95.5 - - - +
17C LEU* 1.3 62.2 + - - +
18C GLY 5.0 2.0 - - - +
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Residues in contact with LEU 17 (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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10C ILE* 2.9 16.4 + - + +
12C VAL* 2.9 41.7 - - + -
15C GLU* 3.4 1.9 + - + +
16C PRO* 1.3 75.8 - - - +
18C GLY* 1.3 60.6 + - - +
138C ILE* 3.8 30.9 - - + +
141C ALA* 3.9 28.5 - - + -
142C MET* 4.4 13.0 - - + +
145C PHE* 4.5 9.4 - - + -
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Residues in contact with GLY 18 (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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9C ASP* 3.6 5.5 - - - -
10C ILE* 2.9 30.2 + - - +
16C PRO* 3.7 2.6 - - - +
17C LEU* 1.3 82.2 - - - +
19C ARG* 1.3 60.0 + - - -
138C ILE* 4.0 15.4 - - - +
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Residues in contact with ARG 19 (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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7C PHE* 3.0 57.5 - - + +
8C PHE 3.1 10.8 - - - +
9C ASP* 2.7 31.9 + - - +
18C GLY* 1.3 72.2 - - - -
20C VAL* 1.3 72.2 + - - +
21C SER* 4.2 2.5 - - - +
134C GLU 4.0 1.6 - - - +
135C GLY* 3.9 8.8 - - - -
138C ILE* 3.8 12.5 - - - +
160C ASP* 4.6 1.0 + - - -
164C LEU* 4.8 13.4 - - - +
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Residues in contact with VAL 20 (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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7C PHE* 3.2 2.5 - - - -
8C PHE* 2.8 37.5 + - + +
10C ILE* 4.1 17.3 - - + -
19C ARG* 1.3 78.3 - - - +
21C SER* 1.3 61.4 + - - +
22C PHE* 3.3 30.1 - - + -
114C ILE* 5.1 0.2 - - + -
132C VAL* 3.7 24.9 - - + -
134C GLU 3.5 3.4 - - - +
135C GLY 4.3 2.5 - - - +
138C ILE* 3.9 26.7 - - + -
139C VAL* 3.9 20.0 - - + -
142C MET* 4.6 3.4 - - + -
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Residues in contact with SER 21 (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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5C THR* 4.2 7.7 - - - +
6C VAL 3.1 15.3 - - - -
7C PHE* 4.0 2.0 - - - +
19C ARG* 4.2 3.6 - - - +
20C VAL* 1.3 74.5 - - - +
22C PHE* 1.3 64.7 + - - +
132C VAL* 3.4 11.8 - - - +
133C LYS* 3.1 24.0 + - - +
134C GLU* 3.0 32.9 + - - +
164C LEU* 4.1 16.6 - - - -
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Residues in contact with PHE 22 (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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4C PRO 3.5 1.0 - - - +
5C THR* 3.4 7.9 - - - -
6C VAL* 3.1 36.3 + - + +
8C PHE* 3.5 44.4 - + - -
20C VAL* 3.3 36.3 - - + -
21C SER* 1.3 77.9 - - - +
23C GLU* 1.3 62.4 + - - +
24C LEU* 3.6 16.2 + - + +
36C PHE* 4.4 11.2 - + + -
98C LEU* 3.7 26.5 - - + -
114C ILE* 3.7 25.1 - - + -
131C LYS 3.1 9.2 - - - +
132C VAL* 4.0 16.6 - - + -
133C LYS* 4.0 4.7 - - - +
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Residues in contact with GLU 23 (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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3C ASN* 4.3 22.5 + - + +
4C PRO 3.9 3.8 - - - +
5C THR* 4.9 1.1 - - - -
22C PHE* 1.3 72.5 - - - +
24C LEU* 1.3 67.0 + - - +
25C PHE* 3.7 26.8 + - + -
130C GLY* 3.1 4.3 - - - -
131C LYS* 2.7 37.4 + - + +
133C LYS* 3.4 42.9 + - + +
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Residues in contact with LEU 24 (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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3C ASN* 3.1 28.2 - - - +
4C PRO* 3.1 32.7 + - + +
6C VAL* 4.1 10.1 - - + -
22C PHE* 4.6 6.5 - - + +
23C GLU* 1.3 74.4 - - - +
25C PHE* 1.3 60.4 + - - +
26C ALA 3.2 2.6 + - - -
33C ALA* 3.3 33.4 - - + +
36C PHE* 3.5 27.6 - - + -
37C ARG* 3.8 24.5 - - + +
98C LEU* 4.0 9.2 - - + -
129C PHE* 3.7 21.3 - - + +
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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