Contacts of the strand formed by residues 58 - 65 (chain A) in PDB entry 1SOZ
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 VAL 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A ALA 4.0 9.4 - - - +
55A ALA 3.0 13.4 + - - +
56A PRO 4.4 1.6 - - - +
57A ALA* 1.3 81.5 - - - +
59A VAL* 1.3 65.3 + - - +
60A ASN* 5.9 0.9 - - - +
81A SER* 4.3 7.2 - - - -
82A GLY 3.1 15.9 - - - +
83A VAL* 4.2 8.5 - - + -
109A GLN* 3.5 22.3 + - - +
141A ILE* 5.0 1.6 - - + -
158A ILE* 3.0 58.3 - - + +
159A GLY* 4.5 2.9 - - - -
166A GLN* 3.6 2.3 - - - +
204A ALA* 4.0 14.8 - - + +
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Residues in contact with VAL 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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56A PRO 5.5 0.7 - - - +
57A ALA 4.0 0.7 - - - +
58A VAL* 1.3 79.1 - - - +
60A ASN* 1.3 81.2 + - - +
61A VAL* 3.8 1.3 - - + -
81A SER* 3.2 10.6 - - - -
82A GLY* 2.7 41.0 + - - +
84A ILE* 3.4 39.3 - - + -
91A ILE* 5.1 2.2 - - + -
106A VAL* 3.0 30.7 - - + -
107A ALA 2.6 25.6 - - - +
108A LEU* 3.6 12.6 - - + -
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Residues in contact with ASN 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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58A VAL* 5.4 1.0 - - - +
59A VAL* 1.3 86.1 + - - +
61A VAL* 1.3 59.4 + - - +
62A TYR* 3.4 30.8 + - + +
80A GLY 3.8 5.4 - - - +
105A ILE 3.4 1.7 - - - +
106A VAL* 3.4 2.8 - - - -
107A ALA* 2.9 36.0 + - + +
109A GLN* 3.4 22.9 + - - +
159A GLY 5.4 1.0 - - - -
160A ASN* 3.3 35.2 + - - +
163A ASN* 4.8 0.3 + - - -
165A GLY* 4.9 5.4 - - - -
166A GLN* 4.9 5.3 + - - +
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Residues in contact with VAL 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 VAL* 4.2 1.6 - - + +
60A ASN* 1.3 76.0 - - - +
62A TYR* 1.3 65.9 + - - +
79A LEU* 3.2 5.5 - - - +
80A GLY 2.7 42.8 + - - +
81A SER 3.2 31.4 - - - +
82A GLY* 3.4 10.5 - - - +
91A ILE* 5.5 0.2 - - + -
93A THR* 4.0 6.7 - - - +
97A VAL* 4.3 7.9 - - + -
98A ILE* 4.0 16.8 - - + -
104A ILE* 3.8 25.6 - - + -
105A ILE 3.4 3.1 - - - +
106A VAL* 4.8 5.8 - - + +
130A LEU* 4.3 11.4 - - + -
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Residues in contact with TYR 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 ASN* 3.4 38.6 + - + +
61A VAL* 1.3 77.4 - - - +
63A ASN* 1.3 61.3 + - - +
64A ARG* 3.8 4.4 + - + -
76A ILE* 4.0 31.4 - - + -
78A THR 3.7 2.2 - - - -
79A LEU* 3.9 22.7 - - + -
103A GLN 3.8 0.7 - - - +
104A ILE* 3.2 9.0 - - - +
105A ILE* 2.9 60.8 + - + +
107A ALA* 4.1 11.4 - - + +
160A ASN* 4.5 0.9 - - - -
163A ASN* 3.3 32.6 + - - -
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Residues in contact with ASN 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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62A TYR* 1.3 71.8 - - - +
64A ARG* 1.3 63.3 + - - +
76A ILE* 3.2 3.8 - - - -
77A ARG* 2.7 46.4 + - - +
78A THR* 2.7 25.7 + - - +
79A LEU* 4.6 0.2 - - - +
97A VAL* 3.0 28.8 - - + +
98A ILE* 3.5 3.9 - - + -
99A ASN 3.2 21.0 + - - +
101A ALA* 2.8 34.3 - - + +
103A GLN 3.9 2.2 - - - -
104A ILE* 4.9 0.9 - - - +
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Residues in contact with ARG 64 (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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62A TYR* 4.4 10.1 - - + +
63A ASN* 1.3 83.0 - - - +
65A GLY* 1.3 58.9 + - - +
74A LEU* 3.0 40.7 + - + +
75A GLU* 3.2 12.6 - - - +
76A ILE* 3.9 30.3 - - + +
102A ASP* 2.9 24.3 + - - +
103A GLN* 2.6 60.8 + - + +
105A ILE* 4.0 15.7 - - + +
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Residues in contact with GLY 65 (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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64A ARG* 1.3 75.2 - - - +
66A LEU* 1.3 63.5 + - - -
67A ASN 3.6 1.8 - - - -
68A THR* 3.5 17.2 + - - -
73A GLN 3.6 3.8 - - - +
74A LEU* 3.5 8.2 - - - -
75A GLU 2.8 30.5 + - - -
77A ARG* 3.5 14.5 - - - +
102A ASP* 3.2 9.0 - - - -
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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