Contacts of the strand formed by residues 54 - 62 (chain A) in PDB entry 4U86
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 ARG 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A PRO* 3.1 20.7 - - - +
53A ALA* 1.3 86.5 - - - +
55A VAL* 1.3 66.5 + - - +
124A ALA* 3.4 40.9 + - + +
125A PHE* 3.2 15.0 - - - +
126A SER* 3.4 24.8 + - - +
129A GLN* 4.6 4.0 + - - -
139A PHE* 4.3 1.6 - - - -
163A GLU* 4.7 3.8 - - - +
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Residues in contact with VAL 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 PRO* 3.8 11.7 - - + -
54A ARG* 1.3 81.0 - - - +
56A ARG* 1.3 61.3 + - - +
57A CYS* 4.1 8.7 - - - -
124A ALA* 3.1 3.7 - - - -
125A PHE* 2.8 59.2 + - + -
138A SER* 4.1 9.6 - - - +
139A PHE* 3.9 23.8 - - + -
161A ARG* 3.6 33.4 - - - +
163A GLU 3.5 8.1 - - - +
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Residues in contact with ARG 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 VAL* 1.3 74.9 - - - +
57A CYS* 1.3 67.9 + - - +
121A ASP* 2.9 37.8 + - - +
123A GLY* 3.5 23.3 - - - +
124A ALA* 3.9 8.1 - - + +
161A ARG 3.6 0.2 - - - -
162A THR* 2.8 39.7 + - - +
163A GLU* 3.0 55.0 + - + +
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Residues in contact with CYS 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 VAL* 4.1 6.5 - - - -
56A ARG* 1.3 82.1 - - - +
58A SER* 1.3 68.6 + - - +
121A ASP* 3.6 5.3 - - - +
122A LEU* 3.0 28.5 + - + +
123A GLY 3.6 4.1 + - - -
125A PHE* 4.1 16.7 - - + -
134A PHE* 4.8 5.2 - - + -
138A SER* 3.6 31.9 - - - +
159A ILE* 4.0 10.5 - - + -
160A LEU 3.1 8.3 - - - +
161A ARG* 3.9 18.4 - - - -
162A THR* 4.1 2.5 - - - -
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Residues in contact with SER 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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57A CYS* 1.3 77.2 - - - +
59A HIS* 1.3 63.9 + - - +
103A PHE* 3.6 22.2 - - - -
104A GLU* 6.1 0.4 - - - +
119A ARG 4.1 3.5 + - - -
120A GLY 3.1 16.6 - - - -
121A ASP* 3.4 19.9 + - - +
122A LEU* 5.0 0.9 - - - -
159A ILE* 3.5 4.7 - - - +
160A LEU* 2.8 35.1 + - - +
162A THR* 4.1 12.5 - - - +
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Residues in contact with HIS 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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58A SER* 1.3 75.4 - - - +
60A LEU* 1.3 61.8 + - - +
61A LEU* 4.0 12.9 - - + +
103A PHE* 3.6 6.3 - - - -
107A ALA* 3.8 4.7 - - - +
111A SER* 4.0 4.5 + - - -
113A OCS 2.8 31.2 + - - +
115A SER* 3.3 17.3 + - - -
120A GLY* 2.9 29.5 + - - -
122A LEU* 3.8 17.4 - - + +
134A PHE* 3.6 23.2 - + + -
157A HIS* 2.9 35.2 + + - +
158A ILE 3.0 14.4 - - - +
159A ILE* 4.4 0.4 - - - -
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Residues in contact with LEU 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 HIS* 1.3 76.0 - - - +
61A LEU* 1.3 63.9 + - - +
62A VAL* 3.8 26.2 - - + -
89A ILE* 4.2 4.8 - - + +
92A TYR* 3.9 26.0 - - + -
96A ILE* 5.3 3.8 - - + -
103A PHE* 3.9 9.6 - - + +
106A LEU* 3.7 40.2 - - + +
107A ALA* 3.7 14.8 - - + +
110A PHE 4.4 1.3 - - - +
111A SER* 3.7 11.2 - - - -
156A ILE 3.8 0.9 - - - +
157A HIS* 3.3 5.1 - - - -
158A ILE* 2.9 43.4 + - + +
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Residues in contact with LEU 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 HIS* 4.0 12.9 + - + -
60A LEU* 1.3 72.8 - - - +
62A VAL* 1.3 64.6 + - - +
63A LYS* 3.9 24.0 - - + -
110A PHE 3.8 0.9 - - - +
111A SER* 3.0 18.5 + - - +
112A ASP* 2.8 48.4 + - - +
113A OCS 4.2 16.6 - - + +
154A SER* 4.0 11.2 - - - +
155A GLY* 3.7 11.0 - - - -
156A ILE 3.5 25.4 - - - +
157A HIS* 3.6 26.9 - - + +
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Residues in contact with VAL 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 LEU* 3.8 12.5 + - + -
61A LEU* 1.3 76.2 - - - +
63A LYS* 1.3 66.7 + - - +
64A HIS* 4.4 0.2 - - - -
80A ARG* 3.6 23.1 - - - +
85A ALA* 3.7 26.6 - - + +
88A LEU* 4.1 8.7 - - + -
89A ILE* 3.7 30.5 - - + -
92A TYR* 3.9 16.6 - - + -
110A PHE 4.7 4.0 - - - +
112A ASP* 3.7 2.5 - - - +
155A GLY* 3.6 0.3 - - - -
156A ILE* 2.8 34.9 + - - +
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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