Contacts of the strand formed by residues 48 - 53 (chain A) in PDB entry 4CY1
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 VAL 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A HIS* 3.9 23.1 - - + -
47A ALA* 1.3 74.7 - - - +
49A SER* 1.3 63.0 + - - +
50A SER 4.0 11.7 - - - +
51A VAL* 4.2 5.4 - - + -
62A SER* 4.5 2.0 - - - -
63A SER 3.3 14.4 - - - +
64A SER* 4.1 1.3 - - - -
305A ILE* 3.2 18.6 - - - +
319A ALA* 3.5 26.5 - - + -
320A ALA 3.2 16.0 + - - +
321A LEU* 3.5 11.1 - - - +
325A LYS* 3.6 26.9 - - - +
327A ILE* 4.2 12.6 - - + -
593D THR* 3.9 0.6 - - - +
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Residues in contact with SER 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA 3.8 0.6 + - - -
48A VAL* 1.3 74.9 - - - +
50A SER* 1.3 59.3 + - - +
63A SER* 2.8 29.7 + - - -
64A SER* 4.6 0.9 - - - -
90A ILE 2.6 29.1 + - - -
91A SER* 3.5 15.2 - - - -
263A PHE* 3.5 5.4 - - - -
305A ILE* 3.7 14.4 - - - +
306A SER* 3.8 0.2 - - - -
592D ARG* 3.2 26.2 - - - +
593D THR* 4.0 15.7 - - - -
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Residues in contact with SER 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 3.9 1.6 - - - +
49A SER* 1.3 84.3 + - - +
51A VAL* 1.3 66.4 + - - +
52A LYS* 3.7 11.8 - - - +
61A ALA 4.0 0.2 - - - +
62A SER* 3.3 3.1 - - - -
63A SER* 2.9 39.0 + - - +
91A SER 4.0 0.2 - - - -
92A ASP* 3.0 31.7 + - - -
93A VAL* 4.0 6.9 + - - +
263A PHE* 3.3 14.8 - - - -
306A SER* 3.6 7.6 - - - -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A VAL* 4.2 0.9 - - + -
50A SER* 1.3 79.7 + - - +
52A LYS* 1.3 75.0 + - - +
60A LEU* 4.2 11.0 - - + -
61A ALA 3.2 4.9 - - - +
62A SER* 3.8 19.5 - - - -
263A PHE* 6.0 0.2 - - - -
306A SER* 3.0 24.8 + - - +
307A THR 4.5 1.0 - - - +
308A ALA* 3.4 13.4 - - + +
317A ALA* 4.1 31.4 - - + +
318A SER 4.5 0.2 - - - -
319A ALA* 3.7 22.2 - - + -
327A ILE* 4.0 15.3 - - + -
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Residues in contact with LYS 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A SER* 3.7 15.3 - - - +
51A VAL* 1.3 80.7 - - - +
53A PHE* 1.3 60.4 + - - +
60A LEU* 3.5 5.5 - - - +
61A ALA 2.8 34.0 + - - +
92A ASP* 3.4 11.7 + - - -
93A VAL* 2.8 41.0 + - + +
94A ALA* 4.1 13.1 - - - +
95A TRP* 3.0 24.8 + - + +
135A CYS 4.5 1.2 + - - -
136A ASN* 4.4 11.5 + - - +
263A PHE* 3.9 21.1 - - - -
307A THR 6.0 0.7 - - - +
308A ALA* 4.2 6.7 - - + -
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Residues in contact with PHE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A LYS* 1.3 73.9 - - - +
54A SER* 1.3 64.5 + - - +
55A PRO* 3.6 2.4 - - - +
57A GLY* 5.5 0.7 - - - -
59A TRP 3.4 3.6 - - - -
60A LEU* 3.7 13.9 - - + -
74A ALA* 3.8 30.5 - - + -
95A TRP* 3.3 10.2 - - - +
308A ALA* 3.5 29.4 - - + +
309A CYS 3.7 6.3 - - - +
310A HIS* 3.5 46.4 - + + -
311A PRO* 4.0 17.7 - - + +
315A ILE* 4.0 12.6 - - + -
317A ALA* 3.6 26.2 - - + -
329A LEU* 3.9 11.2 - - + -
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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