Contacts of the strand formed by residues 53 - 63 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51B ASP 3.8 0.8 + - - -
52B ALA* 1.3 76.7 - - - +
54B VAL* 1.3 61.2 + - - -
55B TYR* 3.2 16.5 - - - -
110B HIS* 4.0 14.0 + - - -
111B LEU 2.8 37.4 + - - -
141B LYS* 4.9 4.7 - - - -
182B ARG* 5.9 0.9 - - - -
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Residues in contact with VAL 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY* 1.3 72.9 - - - -
55B TYR* 1.3 65.0 + - - +
108B VAL* 3.4 29.6 - - + -
109B PHE 3.4 6.5 - - - +
110B HIS* 4.0 11.9 - - + +
141B LYS* 3.9 3.3 - - - +
142B LEU* 3.0 38.5 + - + +
154B CYS* 4.0 5.2 - - - -
180B PHE* 3.6 33.9 - - + -
182B ARG* 3.5 36.7 - - - +
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Residues in contact with TYR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B SER* 4.8 1.6 - - - -
39B GLY* 3.7 13.5 + - - -
40B LEU* 3.9 25.9 - - + +
49B ILE* 4.1 11.2 - - + -
51B ASP* 2.6 30.6 + - - +
53B GLY* 3.2 33.0 - - - -
54B VAL* 1.3 72.6 - - - +
56B LEU* 1.3 65.6 + - - +
57B LEU* 3.7 3.4 + - + +
108B VAL* 3.3 4.3 - - - -
109B PHE* 2.9 34.7 + - - +
111B LEU* 3.7 23.3 - - + -
139B PHE* 4.3 15.7 - - + -
140B VAL 3.3 7.2 - - - +
141B LYS* 3.6 45.2 - - + +
142B LEU* 4.5 4.0 - - - -
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Residues in contact with LEU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 1.3 71.4 - - - +
57B LEU* 1.3 66.0 + - - +
58B TYR* 5.0 4.4 - - + -
106B ALA* 4.7 8.3 - - + -
107B GLY* 3.8 13.5 - - - +
108B VAL* 3.8 23.1 - - + -
138B GLY 4.1 0.3 - - - +
139B PHE* 3.3 4.3 - - - -
140B VAL* 2.8 50.1 + - + +
142B LEU* 4.2 16.4 - - + +
202B PHE* 4.1 26.2 - - + -
204B TYR* 5.5 0.4 - - + -
290B LEU* 4.7 5.6 - - + -
353B PHE* 4.3 34.8 - - + -
441B LEU* 6.4 1.6 - - + -
443B LEU* 6.3 1.1 - - + -
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Residues in contact with LEU 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B TYR* 4.6 4.9 - - + +
56B LEU* 1.3 75.3 - - - +
58B TYR* 1.3 60.3 + - - +
74B VAL* 3.9 9.0 - - + -
85B LEU* 3.7 18.6 - - + -
86B PHE* 3.6 21.9 - - + -
106B ALA* 3.2 4.5 - - - +
107B GLY 3.0 34.8 + - - +
109B PHE* 4.0 7.9 - - + -
111B LEU* 5.0 3.6 - - + -
117B LEU* 3.6 27.1 - - + -
137B LEU* 3.8 25.4 - - + -
138B GLY 3.4 15.5 - - - +
139B PHE* 4.1 21.1 - - + +
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B HIS* 2.7 23.7 + - - -
56B LEU* 5.0 7.9 - - + -
57B LEU* 1.3 75.5 - - - +
59B SER* 1.4 63.9 + - - +
86B PHE* 4.4 1.1 - - - -
104B TYR* 3.1 25.6 - + + +
105B SER 3.6 4.5 - - - -
106B ALA* 3.8 4.5 - - + -
136B PHE* 3.8 23.1 - + - -
137B LEU* 3.5 6.4 - - - +
138B GLY* 3.0 58.4 + - - +
140B VAL* 4.7 2.5 - - + -
353B PHE* 3.8 18.4 - + + -
407B ALA 3.8 11.7 - - - -
408B GLY* 3.6 11.4 - - - -
409B ILE* 2.9 46.9 + - + +
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B TYR* 1.4 78.4 - - - +
60B GLN* 1.3 62.3 + - - +
61B VAL* 4.5 0.3 - - - +
72B GLN* 3.2 28.7 + - - +
74B VAL* 3.8 25.2 - - - +
86B PHE* 4.1 7.0 - - - -
104B TYR* 3.5 4.6 - - - -
105B SER 2.8 34.1 + - - -
119B VAL* 4.1 9.7 - - - +
136B PHE 3.7 7.0 + - - -
137B LEU* 4.0 8.7 - - - -
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Residues in contact with GLN 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B TRP* 4.9 0.2 - - - -
59B SER* 1.3 72.2 + - - +
61B VAL* 1.3 69.8 + - - +
102B SER* 4.0 12.7 + - - -
103B CYS 3.3 21.3 - - - +
104B TYR* 3.8 15.2 - - + +
134B GLY* 3.0 28.6 + - - +
135B THR* 3.2 2.3 - - - +
136B PHE* 2.9 63.3 + - + +
390B ARG 3.1 22.2 + - - +
405B TYR 4.3 1.4 - - - +
406B SER* 2.7 26.9 + - - -
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Residues in contact with VAL 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B VAL* 5.7 0.4 - - + -
30B TRP* 5.6 0.9 - - + -
59B SER* 4.5 1.1 - - - +
60B GLN* 1.3 78.2 - - - +
62B LEU* 1.3 65.4 + - - +
63B PHE* 3.8 26.0 + - + -
72B GLN* 3.6 38.6 - - + +
101B ASN 3.9 0.9 - - - +
102B SER* 3.4 1.7 - - - -
103B CYS* 2.8 34.6 + - - +
119B VAL* 4.2 12.8 - - + -
121B ILE* 4.7 6.3 - - + -
128B LEU* 3.9 18.6 - - + -
134B GLY 3.7 3.1 - - - -
135B THR* 3.7 21.3 - - + +
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Residues in contact with LEU 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL* 1.3 72.0 - - - +
63B PHE* 1.3 61.4 + - - +
64B GLN* 5.3 4.7 - - + +
100B TYR* 5.0 4.0 - - + -
101B ASN 3.7 5.2 - - - +
102B SER* 3.7 19.7 - - - +
128B LEU* 3.3 8.7 - - - +
129B ASN* 3.0 59.4 + - + +
131B SER* 5.4 0.7 - - - -
133B HIS* 6.2 1.3 - - + +
134B GLY* 3.6 22.6 + - - +
135B THR* 3.1 16.0 + - - +
390B ARG* 5.2 8.3 - - + -
392B ILE* 3.3 33.9 - - + -
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Residues in contact with PHE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B VAL* 3.8 16.6 - - + -
62B LEU* 1.3 72.0 - - - +
64B GLN* 1.3 67.7 + - - +
65B ASP* 3.8 1.6 - - - +
70B MET* 3.6 41.5 - - + -
71B GLY* 3.5 28.0 - - - -
72B GLN* 3.7 15.5 - - + -
90B ARG* 4.6 6.7 - - + -
92B MET* 3.7 17.6 - - + +
100B TYR* 3.5 2.9 - - - -
101B ASN 2.8 40.3 + - - +
103B CYS* 3.7 27.6 - - + -
121B ILE* 4.1 6.5 - - + -
127B LYS 3.8 1.3 - - - -
128B LEU* 3.6 28.7 - - + -
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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