Contacts of the strand formed by residues 53 - 63 (chain A) in PDB entry 4ZCH
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 GLY 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ASP 3.9 0.6 + - - -
52A ALA* 1.3 75.7 - - - +
54A VAL* 1.3 66.2 + - - -
55A TYR* 3.4 12.4 - - - -
110A HIS* 4.4 12.2 - - - -
111A LEU 2.9 33.7 + - - -
141A LYS* 4.0 9.6 - - - -
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Residues in contact with VAL 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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53A GLY* 1.3 75.0 - - - -
55A TYR* 1.3 56.1 + - - +
108A VAL* 3.5 28.5 - - + -
109A PHE 3.5 7.0 - - - +
110A HIS* 4.1 10.3 - - + +
141A LYS* 3.5 8.1 - - - +
142A LEU* 2.8 42.8 + - + +
154A CYS* 4.1 4.0 - - - -
180A PHE* 3.5 36.1 - - + -
182A ARG* 3.7 35.9 - - - +
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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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8A SER* 4.5 1.6 - - - -
39A GLY 4.0 9.4 + - - -
40A LEU* 3.7 25.4 - - + +
49A ILE* 4.3 6.0 - - + +
51A ASP* 2.7 41.8 + - - -
53A GLY* 3.4 25.1 - - - -
54A VAL* 1.3 74.2 - - - +
56A LEU* 1.3 64.9 - - - +
57A LEU* 3.8 4.4 + - + +
107A GLY 3.7 0.7 - - - +
108A VAL* 3.3 5.5 - - - -
109A PHE* 2.9 33.0 + - - +
111A LEU* 3.7 34.3 - - + -
139A PHE* 4.2 15.0 - + + -
140A VAL 3.2 6.7 - - - -
141A LYS* 3.5 35.7 - - + -
142A LEU* 4.5 4.0 - - - -
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Residues in contact with LEU 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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55A TYR* 1.3 71.5 - - - +
57A LEU* 1.3 62.0 + - - +
58A TYR* 4.3 6.0 - - + -
106A ALA* 4.6 15.3 - - + -
107A GLY* 3.6 12.6 - - - +
108A VAL* 4.1 17.5 - - + -
138A GLY 4.5 0.2 - - - -
139A PHE* 3.3 5.0 - - - -
140A VAL* 2.8 53.6 + - + +
142A LEU* 4.2 14.3 - - + +
202A PHE* 4.4 24.2 - - + -
204A TYR* 5.6 1.1 - - + -
290A LEU* 4.7 7.4 - - + -
353A PHE* 4.5 29.6 - - + -
441A LEU* 6.3 2.9 - - + -
443A LEU* 6.3 1.3 - - + -
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Residues in contact with LEU 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* 4.7 6.1 - - + +
56A LEU* 1.3 75.7 - - - +
58A TYR* 1.3 60.4 + - - +
74A VAL* 3.9 12.8 - - + -
85A LEU* 3.6 22.0 - - + -
86A PHE* 3.6 13.4 - - + -
106A ALA* 3.1 4.2 - - - +
107A GLY 2.9 36.8 + - - +
109A PHE* 4.2 6.3 - - + -
111A LEU* 5.0 2.7 - - + -
117A LEU* 3.5 26.2 - - + -
137A LEU* 3.8 21.8 - - + -
138A GLY 3.3 17.5 - - - +
139A PHE* 3.6 26.2 - - + -
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Residues in contact with TYR 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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11A HIS* 2.7 24.3 + - - -
56A LEU* 5.1 7.9 - - + -
57A LEU* 1.3 75.6 - - - +
59A SER* 1.3 63.4 + - - +
86A PHE* 4.4 0.7 - - - -
104A TYR* 3.2 26.5 - + + +
105A SER 3.5 4.3 - - - -
106A ALA* 3.8 5.6 - - + -
136A PHE* 3.6 34.8 - + - -
137A LEU* 3.5 5.6 - - - +
138A GLY* 2.9 60.8 + - - +
139A PHE 4.0 0.4 - - - -
140A VAL* 4.8 2.0 - - + -
353A PHE* 3.7 18.6 - + + -
407A ALA 4.2 4.0 - - - -
408A GLY* 3.8 10.1 - - - -
409A ILE* 3.1 41.3 + - + +
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Residues in contact with SER 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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30A TRP* 6.0 0.2 - - - -
58A TYR* 1.3 78.4 - - - +
60A GLN* 1.3 60.6 + - - +
61A VAL* 4.6 0.3 - - - +
72A GLN* 3.3 23.0 + - - +
74A VAL* 3.6 28.7 - - - +
86A PHE* 3.9 9.0 - - - -
104A TYR* 3.4 5.1 - - - -
105A SER 2.9 32.4 + - - +
119A VAL* 4.1 8.3 - - - +
136A PHE* 3.6 7.1 + - - -
137A LEU* 4.2 8.7 - - - -
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Residues in contact with GLN 60 (chain A).
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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59A SER* 1.3 73.0 - - - +
61A VAL* 1.3 70.6 + - - +
102A SER* 3.8 18.3 + - - -
103A CYS 3.2 15.5 - - - +
104A TYR* 3.8 15.7 - - + +
133A HIS 3.6 4.2 + - - -
134A GLY* 2.8 27.1 + - - +
135A THR* 3.3 2.2 - - - +
136A PHE* 2.9 55.6 + - + +
390A ARG 2.9 24.0 + - - +
405A TYR 4.4 1.2 - - - +
406A SER* 2.7 28.9 + - - -
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Residues in contact with VAL 61 (chain A).
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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28A VAL* 5.4 1.3 - - + -
30A TRP* 5.4 1.3 - - + -
59A SER* 4.6 1.6 - - - +
60A GLN* 1.3 78.6 - - - +
62A LEU* 1.3 60.9 + - - +
63A PHE* 3.6 24.3 - - + -
72A GLN* 3.6 36.1 - - + +
102A SER* 3.4 1.1 - - - -
103A CYS 2.8 32.8 + - - -
119A VAL* 4.1 13.7 - - + -
121A ILE* 4.2 4.7 - - + -
128A LEU* 3.8 32.1 - - + -
134A GLY 3.8 2.2 - - - -
135A THR* 3.9 17.3 - - + +
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Residues in contact with LEU 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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61A VAL* 1.3 71.5 - - - +
63A PHE* 1.3 73.6 + - - +
64A GLN* 4.8 2.7 - - + +
100A TYR* 4.3 5.4 - - + -
101A ASN 3.7 12.1 - - - +
102A SER* 3.9 5.2 - - - +
128A LEU* 3.4 5.7 - - - +
129A ASN* 2.8 51.6 + - + +
134A GLY* 3.5 29.4 + - - +
135A THR* 3.1 13.0 + - - +
390A ARG* 3.4 32.5 - - + +
392A ILE* 3.5 31.0 - - + -
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Residues in contact with PHE 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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61A VAL* 3.6 24.2 - - + -
62A LEU* 1.3 74.7 - - - +
64A GLN* 1.3 65.4 + - - +
65A ASP* 3.6 5.4 - - - +
70A MET* 3.6 35.2 - - + -
71A GLY* 3.7 23.1 - - - -
72A GLN* 3.6 15.0 - - - -
90A ARG* 5.0 6.1 - - + -
92A MET* 3.8 19.5 - - + +
100A TYR* 3.5 3.1 - - - -
101A ASN 3.1 41.9 + - - +
103A CYS* 3.6 21.8 - - + -
121A ILE* 4.1 9.0 - - + -
127A LYS 3.8 2.5 - - - -
128A LEU* 3.5 26.7 - - + -
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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