Contacts of the strand formed by residues 25 - 31 (chain P) in PDB entry 2ZJQ
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 PHE 25 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P LYS* 3.5 53.8 + - + +
23P PRO 3.2 3.6 - - - +
24P GLY* 1.3 78.0 - - - +
26P ALA* 1.3 66.2 + - - +
27P VAL* 3.7 35.7 - - + -
75P ALA* 4.1 2.9 - - - -
78P ASN* 3.4 20.1 - - - +
96P TYR* 4.3 14.8 - - - -
125P THR* 4.4 7.2 - - + -
126P ILE 3.9 1.8 - - - -
127P ILE* 3.4 32.3 - - + -
504X G 4.0 0.4 - - - -
505X G 3.7 30.0 - - - +
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Residues in contact with ALA 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P PHE* 1.3 82.4 - - - +
27P VAL* 1.3 63.6 + - - +
71P VAL* 3.8 12.3 - - + +
74P SER* 3.9 9.0 - - - +
75P ALA* 3.3 33.4 - - + +
78P ASN* 4.6 1.3 - - - +
125P THR* 3.1 4.5 - - - -
126P ILE 2.8 30.4 + - - +
503X G 5.9 0.9 - - - +
504X G 3.6 12.6 - - - +
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Residues in contact with VAL 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25P PHE* 3.7 15.5 - - + -
26P ALA* 1.3 77.6 - - - +
28P ALA* 1.3 65.3 + - - +
29P LYS* 3.9 17.9 - - + -
71P VAL* 4.1 3.1 - - - +
123P HIS* 4.7 3.4 - - + -
124P ILE 3.4 5.6 - - - +
125P THR* 3.2 30.1 - - + -
503X G 2.7 26.3 + - - +
504X G 3.2 45.3 + - - +
505X G 5.0 0.2 - - - +
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Residues in contact with ALA 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27P VAL* 1.3 75.8 - - - +
29P LYS* 1.3 61.2 + - - +
31P VAL* 3.7 19.7 - - + +
67P PRO* 6.2 0.7 - - + -
71P VAL* 3.3 29.1 - - + +
123P HIS* 3.2 4.2 - - - -
124P ILE* 2.7 30.2 + - + +
502X A 4.5 15.3 - - + +
503X G 3.7 6.7 - - - -
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Residues in contact with LYS 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27P VAL* 3.9 21.3 - - + -
28P ALA* 1.3 72.3 - - - +
30P TYR* 1.3 87.5 + - + +
31P VAL* 3.4 2.3 + - - +
123P HIS* 3.3 35.5 + - + +
24X G 5.0 11.1 + - - -
25X U 4.5 9.1 + - - -
502X A 4.7 6.4 + - - +
503X G 3.0 39.7 + - - +
504X G 3.5 20.3 + - - +
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Residues in contact with TYR 30 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29P LYS* 1.3 96.2 + - + +
31P VAL* 1.3 65.9 + - - +
32P ARG* 3.0 7.8 + - - +
101P PRO* 3.4 26.7 - - + -
121P THR* 4.4 13.2 - - + +
122P SER 3.5 1.5 + - - -
123P HIS* 3.0 25.9 + + - -
25X U 5.4 3.7 + - - -
502X A 5.1 4.9 - - - +
503X G 4.2 13.0 - - - -
504X G 5.9 0.2 - - - -
518X A 2.8 85.3 + + - +
519X C 5.1 2.1 + - - -
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Residues in contact with VAL 31 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28P ALA* 3.7 30.1 - - + +
29P LYS 4.5 1.1 - - - +
30P TYR* 1.3 68.5 - - - +
32P ARG* 1.3 53.8 + - - +
33P MET* 2.6 32.6 + - + +
67P PRO* 4.1 28.9 - - + -
121P THR* 3.3 1.0 - - - -
122P SER* 2.7 46.2 + - - +
124P ILE* 3.7 22.7 - - + -
502X A 5.9 2.2 - - + -
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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