Contacts of the strand formed by residues 58 - 63 (chain A) in PDB entry 4P7A
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 LEU 58 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 4.7 5.2 - - + +
51A VAL* 3.4 4.2 - - - -
52A LYS* 2.9 38.7 + - + +
55A GLY* 3.7 2.9 + - - -
56A LEU 3.8 0.8 - - - -
57A LYS* 1.3 83.7 - - + +
59A ILE* 1.3 97.3 + - - +
60A GLN* 4.0 18.6 - - + +
151A THR* 3.5 25.1 - - + -
152A VAL 3.5 3.8 - - - -
153A GLU* 4.1 14.6 - - + +
197A GLN* 3.5 35.0 - - + +
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Residues in contact with ILE 59 (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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28A PRO* 4.1 21.5 - - + +
31A ALA* 4.5 8.7 - - + -
32A ILE* 3.6 35.9 - - + -
35A MET* 3.9 14.6 - - + -
49A VAL* 4.9 2.2 - - + -
50A ILE 3.5 5.6 - - - +
51A VAL* 4.7 2.0 - - + -
55A GLY* 3.7 25.8 - - - +
58A LEU* 1.3 83.5 - - - +
60A GLN* 1.3 63.1 + - - +
61A ILE* 4.1 9.9 - - + -
150A ILE 3.8 0.7 - - - +
151A THR* 3.3 0.7 - - - -
152A VAL* 2.7 54.9 + - + +
155A LEU* 4.9 3.4 - - + -
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Residues in contact with GLN 60 (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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49A VAL* 3.4 4.2 - - - +
50A ILE* 2.8 62.6 + - + +
58A LEU* 4.0 15.8 - - + +
59A ILE* 1.3 75.1 - - - +
61A ILE* 1.3 65.0 + - - +
149A GLN* 3.6 30.7 + - + +
150A ILE 3.3 2.5 - - - -
151A THR* 3.1 29.8 + - - +
197A GLN* 5.8 2.0 - - - +
405A UNX 3.4 8.7 - - - -
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Residues in contact with ILE 61 (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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32A ILE* 4.2 20.0 - - + +
35A MET* 3.8 38.1 - - + -
36A ILE* 4.3 5.2 - - + -
39A CYS* 3.8 27.5 - - - -
47A ILE* 3.9 14.6 - - + -
48A GLN 3.2 7.4 - - - +
49A VAL* 4.1 17.7 - - + -
59A ILE* 4.1 12.3 - - + -
60A GLN* 1.3 79.3 - - - +
62A GLN* 1.3 59.5 + - - +
63A ASP* 5.4 0.5 - - - +
148A THR 3.5 2.8 - - - +
149A GLN* 3.2 4.1 - - - -
150A ILE* 2.9 36.7 + - + +
405A UNX 4.1 0.4 - - - -
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Residues in contact with GLN 62 (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 ILE* 3.5 4.7 - - - +
48A GLN* 2.8 52.9 + - + +
61A ILE* 1.3 74.1 - - - +
63A ASP* 1.3 82.7 + - - +
145A ASN 5.2 4.8 + - - +
146A GLN 4.9 2.4 + - - -
147A GLY 4.5 2.2 - - - -
148A THR 3.4 17.6 + - - +
149A GLN* 3.3 29.0 - - + +
405A UNX 3.5 15.2 - - - -
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Residues in contact with ASP 63 (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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39A CYS* 3.3 20.8 - - + -
44A SER* 3.1 25.5 + - - +
46A SER 3.4 8.7 - - - +
47A ILE* 4.3 1.1 - - + -
48A GLN* 5.6 0.7 - - - -
62A GLN* 1.3 95.3 + - - +
64A ASN* 1.3 58.0 - - - +
65A GLY* 2.9 15.0 + - - -
146A GLN 3.7 1.0 - - - +
147A GLY* 3.6 2.8 - - - -
148A THR* 2.7 36.7 + - - +
150A ILE* 6.0 0.2 - - - +
402A ADP 2.9 31.0 + - - -
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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