Contacts of the strand formed by residues 53 - 62 (chain A) in PDB entry 4Z4H
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 ASP 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A ILE* 1.3 89.6 - - + +
54A ILE* 1.3 60.8 + - - +
55A TYR* 3.8 19.0 + - + +
103A ALA 3.7 9.5 - - - +
137A CYS* 4.5 18.3 - - + +
138A VAL 3.5 6.6 - - - +
139A SER* 3.2 29.8 + - - +
141A GLN* 6.5 0.2 - - - -
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Residues in contact with ILE 54 (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 ILE* 4.0 3.4 - - + +
53A ASP* 1.3 78.6 - - - +
55A TYR* 1.3 64.6 + - - +
101A TYR* 4.5 8.1 - - + -
102A THR 3.6 10.5 - - - +
103A ALA* 4.6 5.4 - - + +
137A CYS* 3.6 1.7 - - - -
138A VAL* 2.7 56.3 + - + +
140A LEU* 3.9 31.9 - - + -
161A ALA* 3.8 30.3 - - + -
162A LEU* 5.4 1.8 - - + +
165A VAL* 5.5 2.5 - - + -
397A PHE* 3.8 33.4 - - + -
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Residues in contact with TYR 55 (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 ILE* 6.1 0.2 - - + -
53A ASP* 3.8 19.7 + - + +
54A ILE* 1.3 72.8 - - - +
56A HIS* 1.3 61.2 - - - +
57A TYR* 3.8 10.7 - - + +
100A LEU 3.6 1.4 - - - +
101A TYR* 3.3 7.7 - - - -
102A THR* 2.9 48.6 + - - +
103A ALA 3.7 13.2 - - - -
104A MET* 3.6 7.9 - - - -
105A PRO* 3.4 53.0 - - + +
134A TRP* 3.4 30.5 - + + -
136A SER 4.1 2.2 - - - -
137A CYS* 4.0 17.5 - - + -
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Residues in contact with HIS 56 (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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54A ILE 3.9 0.8 + - - -
55A TYR* 1.3 72.9 - - - +
57A TYR* 1.3 97.1 + - - +
58A GLU* 4.6 1.8 + - - +
99A ASN* 2.4 31.4 + - + -
100A LEU 3.6 3.6 - - - -
101A TYR* 3.8 32.8 + + + -
134A TRP* 4.0 1.7 - - - -
135A VAL* 3.2 39.3 + - + +
136A SER* 3.0 38.2 + - - +
138A VAL* 4.2 10.6 - - + +
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Residues in contact with TYR 57 (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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55A TYR* 3.8 16.6 - - + +
56A HIS* 1.3 82.4 - - - +
58A GLU* 1.3 65.1 + - - +
59A LEU* 3.5 8.8 - - + +
98A LYS 3.5 2.3 - - - +
100A LEU* 2.7 51.3 + - + +
102A THR* 3.5 19.5 - - + -
105A PRO* 3.8 8.1 - - - +
106A LEU* 3.0 45.9 + - + +
108A ILE* 2.8 34.5 - - + +
132A ILE* 4.3 7.0 - - + -
133A LYS 3.5 3.4 - - - +
134A TRP* 3.5 44.8 - + + -
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Residues in contact with GLU 58 (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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56A HIS* 5.0 2.7 - - + +
57A TYR* 1.3 70.0 - - - +
59A LEU* 1.3 82.1 + - - +
98A LYS* 3.2 21.1 - - + +
99A ASN* 5.9 0.7 - - - +
132A ILE* 3.5 3.5 - - - +
133A LYS* 2.6 50.9 + - + +
135A VAL* 3.4 25.9 - - + +
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Residues in contact with LEU 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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57A TYR* 3.5 11.0 - - + +
58A GLU* 1.3 99.8 - - - +
60A ASP* 1.3 65.5 + - - +
61A ILE* 5.3 3.4 - - + -
75A VAL* 3.8 20.9 - - + -
78A MET* 4.6 7.2 - - + -
94A PHE* 3.6 24.0 - - + -
97A ARG 4.6 2.7 - - - +
98A LYS* 2.8 39.2 + - - +
100A LEU* 3.3 41.1 - - + +
130A VAL* 4.7 5.6 - - + -
131A SER* 3.3 11.0 - - - +
132A ILE* 4.3 10.3 - - + -
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Residues in contact with ASP 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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59A LEU* 1.3 77.0 - - - +
61A ILE* 1.3 86.0 + - - +
62A LYS* 4.0 23.5 - - - +
64A GLU* 3.4 23.3 - - - +
97A ARG 5.8 0.4 - - - -
98A LYS* 5.4 6.5 - - - +
129A LYS 3.4 1.9 - - - +
130A VAL* 3.2 6.8 - - - +
131A SER* 2.9 49.2 + - - +
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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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59A LEU* 5.3 2.5 - - + -
60A ASP* 1.3 85.7 + - - +
62A LYS* 1.3 60.9 + - - +
63A PRO 2.9 21.5 - - - +
64A GLU* 3.1 16.7 + - + +
71A ASN* 3.8 48.0 - - + +
74A ILE* 3.6 36.6 - - + -
75A VAL* 4.5 10.5 - - + -
94A PHE* 4.5 7.2 - - + -
97A ARG 4.6 4.7 - - - +
128A PHE* 3.8 13.5 - - + -
129A LYS 3.5 3.1 - - - +
130A VAL* 4.1 16.6 - - + -
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Residues in contact with LYS 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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60A ASP* 4.0 24.2 - - - +
61A ILE* 1.3 74.3 - - - +
63A PRO* 1.3 64.2 - - + +
64A GLU* 4.2 3.4 - - + +
114A GLU* 5.5 3.5 + - - +
127A ILE 4.4 0.5 - - - +
128A PHE* 3.7 6.4 - - - -
129A LYS* 3.0 46.3 + - + +
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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