Contacts of the strand formed by residues 54 - 63 (chain A) in PDB entry 1UWF
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 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A PHE* 3.5 25.2 - - + +
46A ASN* 3.1 22.5 - - - +
52A ILE* 3.7 0.7 - - - +
53A THR* 1.3 73.1 - - - +
55A TYR* 1.3 63.0 + - - +
56A VAL* 5.0 0.2 - - + -
93A VAL 3.7 0.3 - - - +
94A VAL* 3.4 6.6 - - - +
95A TYR* 2.9 42.0 + - + +
133A GLN* 3.5 7.4 + - + -
134A THR 3.5 3.1 - - - +
135A ASN* 3.6 4.7 - - - +
1159A DEG 2.5 51.8 + - - -
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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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53A THR* 3.7 21.5 - - + +
54A ASP* 1.3 75.6 - - - +
56A VAL* 1.3 63.2 + - - +
57A THR* 4.3 0.8 - - - +
92A ARG* 3.6 51.1 - - + -
93A VAL 3.7 2.5 - - - -
94A VAL* 3.9 17.7 - - + -
132A ARG 3.5 1.0 - - - +
133A GLN* 3.3 6.2 - - - -
134A THR* 2.8 45.8 + - - +
135A ASN* 3.5 36.3 - - - -
136A ASN* 3.4 23.1 + - + +
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Residues in contact with VAL 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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1A PHE* 3.6 26.2 - - + -
55A TYR* 1.3 81.0 - - - +
57A THR* 1.3 64.0 + - - +
77A TYR* 2.8 15.1 + - - +
92A ARG* 3.6 0.9 - - - +
93A VAL 2.8 32.4 + - - +
95A TYR* 3.4 34.1 - - + -
103A TRP* 3.6 19.1 - - + +
131A LEU* 3.4 34.8 - - + -
132A ARG 3.3 2.0 - - - -
133A GLN* 4.4 5.8 - - + -
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Residues in contact with THR 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 5.5 0.4 - - - -
56A VAL* 1.3 75.2 - - - +
58A LEU* 1.3 59.8 + - - +
59A GLN 3.7 0.9 + - - -
77A TYR* 3.7 7.9 - - - -
89A GLU* 2.6 33.4 + - + +
90A THR* 3.4 26.7 - - - +
91A PRO 4.1 0.4 - - - -
92A ARG* 3.6 32.5 - - + -
103A TRP* 4.0 1.1 - - - -
131A LEU* 3.4 6.6 - - - -
132A ARG* 3.0 38.7 + - - +
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Residues in contact with LEU 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 THR* 1.3 72.2 - - - +
59A GLN* 1.3 60.0 + - - +
60A ARG 3.5 28.0 - - - +
61A GLY* 5.3 0.9 - - - -
75A VAL* 3.7 39.9 - - + -
77A TYR* 3.9 15.3 - - + -
86A THR* 4.3 9.6 - - + -
88A SER 4.5 1.2 - - - +
89A GLU* 3.7 0.7 - - - -
90A THR* 3.0 46.1 + - + +
103A TRP* 3.9 24.2 - - + -
105A VAL* 4.5 6.5 - - + -
129A LEU* 4.2 11.4 - - + -
130A ILE 3.6 10.3 - - - +
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Residues in contact with GLN 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 THR 3.4 3.0 - - - -
58A LEU* 1.3 74.7 - - - +
60A ARG* 1.3 70.8 + - + +
88A SER 4.0 4.9 - - - +
89A GLU* 3.6 36.2 + - + +
130A ILE* 2.8 27.2 + - + +
132A ARG* 3.6 42.6 + - + +
143A GLN* 2.7 36.6 + - - +
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Residues in contact with ARG 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 LEU* 3.4 10.3 - - - +
59A GLN* 1.3 90.5 + - + +
61A GLY* 1.3 63.1 + - - +
62A SER* 3.9 19.1 - - - +
86A THR* 3.4 15.7 - - - +
128A VAL 3.8 1.5 - - - +
129A LEU* 3.6 0.5 - - - -
130A ILE* 2.9 58.7 + - + +
143A GLN* 4.5 11.3 - - - +
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Residues in contact with GLY 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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58A LEU* 4.7 1.3 - - - -
60A ARG* 1.3 75.7 - - - +
62A SER* 1.3 62.9 + - - -
84A PHE* 3.6 8.1 - - - -
85A PRO* 3.4 5.7 - - - +
86A THR* 2.8 46.7 + - - +
128A VAL 3.5 6.1 - - - -
129A LEU* 3.9 14.8 - - - -
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Residues in contact with SER 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 ARG* 3.9 20.1 + - - +
61A GLY* 1.3 76.6 + - - -
63A ALA* 1.3 60.4 + - - +
64A TYR* 3.6 26.4 + - - -
84A PHE* 3.7 4.5 - - - -
85A PRO* 4.7 4.9 - - - +
127A ALA* 3.1 9.9 - - - +
128A VAL* 3.0 34.4 + - - -
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Residues in contact with ALA 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 SER* 1.3 72.3 - - - +
64A TYR* 1.3 75.6 + - - +
67A VAL* 4.0 6.1 - - + +
68A LEU* 3.8 39.0 - - + +
84A PHE* 3.8 21.0 - - + -
85A PRO* 4.0 22.5 - - + +
126A ILE 3.7 4.9 - - - -
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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