Contacts of the strand formed by residues 40 - 48 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32D SER* 2.7 26.7 + - - +
33D LEU 3.6 5.8 - - - -
34D ASN* 4.0 5.3 - - - +
39D TYR* 1.3 84.5 - - - +
41D PHE* 1.3 63.1 + - - +
42D CYS 3.1 26.0 + - - -
43D GLY* 4.4 1.3 - - - -
66D ARG* 5.6 3.1 - - - +
73D ILE* 4.8 15.5 - - + +
141D TRP* 3.7 43.2 - + + +
151D TYR* 6.4 0.4 - + - -
193D GLY* 3.0 30.6 + - - -
36J LYS* 3.4 25.6 + - + +
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Residues in contact with PHE 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 3.1 46.0 + - + -
34D ASN 3.5 9.2 - - - -
37D SER* 3.1 26.5 - - - -
39D TYR* 3.5 22.7 - - + -
40D HIS* 1.3 77.1 - - - +
42D CYS* 1.3 85.8 + - + +
58D CYS* 3.0 29.4 - - + -
60D LYS* 3.6 28.7 - - + -
63D ILE* 4.0 11.7 - - + -
193D GLY* 4.5 1.5 - - - -
35J VAL* 3.5 8.2 - - + +
36J LYS* 3.3 35.0 + - - +
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Residues in contact with CYS 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D LEU* 2.8 33.2 + - + -
40D HIS* 3.1 18.4 + - - -
41D PHE* 1.3 102.8 - - + +
43D GLY* 1.3 62.5 + - - +
58D CYS* 2.0 53.6 - - + -
193D GLY 4.1 6.3 - - - -
195D SER* 3.4 9.2 - - - +
35J VAL* 3.6 15.3 - - - -
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Residues in contact with GLY 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D GLN* 4.3 8.5 - - - -
31D VAL 3.1 14.1 - - - -
32D SER* 4.5 0.7 - - - -
33D LEU* 3.6 11.8 - - - +
40D HIS* 4.6 3.4 - - - -
42D CYS* 1.3 76.1 - - - +
44D GLY* 1.3 58.4 + - - -
54D SER* 2.9 18.5 + - - -
141D TRP* 5.8 0.4 - - - -
193D GLY 4.5 2.6 + - - -
194D ASP* 4.8 1.3 + - - -
195D SER 2.8 11.6 + - - +
196D GLY 3.4 6.7 - - - +
197D GLY* 4.2 5.2 - - - -
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Residues in contact with GLY 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR 3.7 1.4 - - - +
30D GLN* 3.9 4.1 + - - +
31D VAL* 3.0 36.8 + - - -
33D LEU* 5.2 0.2 - - - -
43D GLY* 1.3 75.5 - - - -
45D SER* 1.3 65.5 + - - -
52D VAL* 4.3 2.5 - - - -
53D VAL 3.5 7.4 - - - -
54D SER* 4.0 3.1 - - - -
196D GLY 3.1 14.8 + - - -
197D GLY* 4.0 2.8 - - - -
198D PRO* 4.1 4.7 - - - +
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Residues in contact with SER 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D TYR* 3.4 7.0 - - - -
31D VAL* 5.0 0.4 - - - -
44D GLY* 1.3 75.5 - - - -
46D LEU* 1.3 61.2 + - - +
47D ILE 3.5 0.6 + - - -
52D VAL* 3.2 6.3 - - - -
53D VAL* 2.8 50.3 + - - +
121D ILE* 4.0 13.0 - - - -
196D GLY 4.7 0.5 + - - -
197D GLY 4.4 1.0 - - - -
198D PRO* 3.0 33.3 - - - +
209D LEU* 3.4 15.5 - - - +
212D ILE* 6.1 0.3 - - - +
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Residues in contact with LEU 46 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29D TYR* 3.0 16.6 + - - +
31D VAL* 4.3 7.8 - - + +
45D SER* 1.3 72.0 - - - +
47D ILE* 1.3 59.7 + - - +
48D ASN 3.6 17.7 - - - +
49D SER 4.2 9.2 - - - +
51D TRP 3.3 19.3 - - - +
52D VAL* 3.9 15.5 - - + +
67D LEU* 3.6 16.2 - - + -
108D LEU* 4.5 1.6 - - + -
112D ALA* 4.2 2.7 - - + -
114D LEU* 4.0 17.0 - - + -
118D VAL* 3.3 34.5 - - + -
119D ALA 4.3 8.3 - - - +
120D SER* 3.1 4.6 - - - -
121D ILE* 2.8 29.7 + - - +
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Residues in contact with ILE 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D SER 3.5 0.9 + - - +
46D LEU* 1.3 74.4 - - - +
48D ASN* 1.3 72.8 + - + +
51D TRP* 3.1 13.1 + - + +
53D VAL* 3.4 42.6 - - + +
105D LEU* 4.4 4.0 - - + -
120D SER* 3.3 12.4 + - - -
121D ILE* 3.9 14.5 - - + +
123D LEU* 3.7 41.3 - - + -
209D LEU* 4.7 3.6 - - + -
238D ILE* 3.9 16.8 - - + -
242D ILE* 4.5 10.3 - - + -
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Residues in contact with ASN 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46D LEU* 3.4 8.5 - - - +
47D ILE* 1.3 89.3 - - + +
49D SER* 1.3 62.2 + - - +
50D GLN* 2.5 31.2 + - - +
51D TRP* 2.8 44.7 + - - +
114D LEU* 4.8 2.2 - - + -
120D SER* 3.7 11.4 - - - +
242D ILE* 4.5 9.5 - - - +
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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