Contacts of the strand formed by residues 40 - 48 (chain F) in PDB entry 1C9T
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 HIS 40 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32F SER* 2.8 26.9 + - - +
33F LEU 3.7 5.2 - - - -
34F ASN* 4.1 4.6 - - - +
39F TYR* 1.3 87.4 - - - +
41F PHE* 1.3 62.7 + - - +
42F CYS 2.8 27.4 + - - -
43F GLY* 4.3 1.6 - - - -
66F ARG* 5.6 3.1 - - - +
73F ILE* 4.9 16.7 - - + +
140F GLY* 6.2 0.2 - - - -
141F TRP* 3.8 43.4 - + + +
193F GLY* 3.0 31.4 + - - -
36L LYS* 3.8 19.7 + - + +
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Residues in contact with PHE 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 3.1 46.0 + - + -
34F ASN 3.6 3.6 - - - -
37F SER* 3.1 31.9 - - - -
39F TYR* 3.7 19.5 - - + -
40F HIS* 1.3 79.1 - - - +
42F CYS* 1.3 88.1 + - + +
58F CYS* 2.9 29.8 - - - -
60F LYS* 3.4 35.9 - - + -
63F ILE* 4.0 8.3 - - + -
193F GLY* 4.4 2.2 - - - -
35L VAL* 3.7 7.0 - - + -
36L LYS* 3.3 31.6 + - - +
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Residues in contact with CYS 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 2.9 25.2 + - + -
40F HIS* 2.8 24.0 + - - -
41F PHE* 1.3 110.6 - - + +
43F GLY* 1.3 64.8 + - - +
58F CYS* 2.0 55.0 - - + -
193F GLY 4.1 6.5 - - - -
195F SER* 3.6 7.2 - - - +
35L VAL* 3.9 10.1 - - - -
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Residues in contact with GLY 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30F GLN* 4.3 8.3 - - - -
31F VAL 3.2 14.6 - - - -
32F SER* 4.5 0.2 - - - -
33F LEU* 3.5 12.9 - - - +
40F HIS* 4.3 3.8 - - - -
42F CYS* 1.3 76.0 - - - +
44F GLY* 1.3 58.3 + - - -
54F SER* 3.0 18.0 + - - -
193F GLY 4.5 1.8 + - - -
194F ASP* 4.8 0.9 + - - -
195F SER 2.9 12.5 + - - -
196F GLY* 3.6 7.1 - - - -
197F GLY* 4.2 5.4 - - - -
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Residues in contact with GLY 44 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR 3.8 0.9 - - - +
30F GLN* 3.8 3.4 + - - -
31F VAL* 3.1 37.9 + - - -
33F LEU* 5.1 0.4 - - - -
43F GLY* 1.3 74.2 - - - -
45F SER* 1.3 64.6 + - - -
52F VAL* 4.2 3.8 - - - -
53F VAL 3.4 9.0 - - - -
54F SER* 4.1 2.0 - - - -
196F GLY 3.2 14.9 + - - -
197F GLY* 4.2 1.8 - - - -
198F PRO* 4.3 4.4 - - - +
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Residues in contact with SER 45 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR* 3.4 6.3 - - - -
31F VAL* 4.8 0.4 - - - -
44F GLY* 1.3 74.8 - - - -
46F LEU* 1.3 62.6 + - - +
47F ILE 3.4 0.3 + - - -
52F VAL* 3.2 6.9 - - - +
53F VAL* 2.9 48.0 + - - +
121F ILE* 3.9 20.0 - - - -
196F GLY 4.3 0.9 + - - -
197F GLY 4.5 0.7 - - - -
198F PRO* 2.8 36.8 - - - +
209F LEU* 3.7 5.3 - - - +
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Residues in contact with LEU 46 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29F TYR* 2.9 17.5 + - - +
31F VAL* 4.3 7.5 - - + +
45F SER* 1.3 70.0 - - - +
47F ILE* 1.3 58.5 + - - +
48F ASN 3.3 28.9 - - - +
49F SER 4.0 9.4 - - - +
51F TRP 3.4 9.2 - - - +
52F VAL* 4.1 13.9 - - + +
67F LEU* 3.7 16.6 - - + -
108F LEU* 4.5 1.3 - - + -
112F ALA* 4.3 1.8 - - + -
114F LEU* 4.0 16.2 - - + -
118F VAL* 3.3 34.8 - - + -
119F ALA 4.0 10.8 - - - +
120F SER* 3.2 4.0 - - - -
121F ILE* 2.9 29.3 + - - +
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Residues in contact with ILE 47 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F SER 3.4 1.3 + - - +
46F LEU* 1.3 75.3 - - - +
48F ASN* 1.3 72.6 + - + +
51F TRP* 3.0 14.3 + - + +
53F VAL* 3.4 42.2 - - + +
105F LEU* 4.5 3.1 - - + -
120F SER* 3.6 10.4 + - - -
121F ILE* 3.9 12.5 - - + +
123F LEU* 3.7 42.6 - - + -
209F LEU* 4.5 4.5 - - + -
238F ILE* 3.9 16.8 - - + -
242F ILE* 4.4 10.8 - - + -
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Residues in contact with ASN 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B ILE 4.6 3.4 + - - -
243B ALA* 3.7 26.9 + - + +
46F LEU* 3.3 10.0 - - - +
47F ILE* 1.3 89.2 - - + +
49F SER* 1.3 79.2 + - - +
50F GLN* 2.7 11.8 + - - +
51F TRP* 2.9 43.3 + - - +
114F LEU* 4.7 0.7 - - - -
120F SER* 3.7 13.0 - - - +
242F ILE* 4.4 9.3 - - - +
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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