Contacts of the strand formed by residues 47 - 56 (chain A) in PDB entry 5UHE
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 PRO 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A SER 3.8 6.7 - - - +
46A ILE* 1.3 94.4 - - + +
48A GLY* 1.3 58.8 + - - +
142A ARG* 4.1 16.8 + - - +
143A GLY 3.5 11.2 - - - +
144A ARG* 4.0 10.3 - - + -
170A PRO* 3.6 12.5 - - - +
202A ILE* 4.9 5.5 - - - +
210A SER* 3.5 25.6 - - - +
228B GLU* 5.1 8.4 - - - +
229B ALA* 4.2 22.2 - - + +
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Residues in contact with GLY 48 (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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46A ILE 3.9 0.4 + - - -
47A PRO* 1.3 76.1 - - - +
49A ALA* 1.3 60.7 + - - -
142A ARG* 3.3 17.7 - - - +
143A GLY 2.8 33.5 + - - +
168A TYR* 3.9 14.1 + - - -
170A PRO* 4.7 5.6 - - - -
201A SER* 6.0 1.3 - - - -
202A ILE* 6.2 1.8 - - - -
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Residues in contact with ALA 49 (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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48A GLY* 1.3 75.1 - - - +
50A ALA* 1.3 63.3 + - - +
85A VAL* 3.0 26.8 + - - +
86A SER* 4.4 1.6 - - - +
87A SER* 3.6 37.9 - - - +
140A VAL* 4.1 4.9 - - + -
141A GLU 3.1 20.0 - - - +
142A ARG* 4.3 4.3 - - + +
167A ILE 5.1 0.3 - - - +
168A TYR* 4.0 10.6 + - - +
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Residues in contact with ALA 50 (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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49A ALA* 1.3 78.0 - - - +
51A VAL* 1.3 68.4 + - - +
52A THR* 3.7 3.2 + - - +
83A LEU 5.5 6.1 - - - +
85A VAL* 4.6 8.5 - - - +
140A VAL* 3.3 9.5 - - - +
141A GLU 3.3 25.4 + - - +
166A SER* 4.7 0.9 - - - -
167A ILE 4.2 31.0 - - - +
168A TYR* 4.0 10.4 - - + -
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Residues in contact with VAL 51 (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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50A ALA* 1.3 77.3 - - - +
52A THR* 1.3 64.1 + - - +
53A SER 3.6 16.6 - - - +
54A ILE* 3.6 19.3 - - + -
80A LEU* 4.7 12.3 - - + +
83A LEU* 3.8 30.7 + - + +
85A VAL* 4.8 3.4 - - + -
138A LEU* 4.0 14.1 - - + -
139A VAL 3.3 15.0 - - - +
140A VAL* 4.4 10.1 - - + -
164A VAL* 4.1 9.4 - - + +
165A ASP 4.0 9.2 - - - +
166A SER* 3.3 16.8 + - - -
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Residues in contact with THR 52 (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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50A ALA 4.0 2.5 - - - +
51A VAL* 1.3 77.2 - - - +
53A SER* 1.3 69.0 + - - +
139A VAL* 3.1 18.3 + - - +
141A GLU* 3.6 52.4 + - + +
152A ASN* 4.6 11.5 + - - +
163A PRO* 3.6 1.0 - - - +
164A VAL* 2.6 40.4 + - - +
166A SER* 3.8 8.3 - - - +
168A TYR* 3.9 15.5 - - - +
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Residues in contact with SER 53 (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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51A VAL* 3.6 1.9 - - - +
52A THR* 1.3 86.4 + - - +
54A ILE* 1.3 72.7 + - - +
139A VAL* 3.0 38.5 + - - +
152A ASN* 4.2 17.1 + - - -
161A ARG* 4.5 15.4 - - - +
162A ILE 3.7 15.3 - - - -
163A PRO* 4.0 9.9 - - - -
164A VAL* 4.1 0.9 - - - +
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Residues in contact with ILE 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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51A VAL* 3.6 19.7 - - + -
53A SER* 1.3 81.3 + - - +
55A ARG* 1.3 68.5 + - - +
56A ILE* 4.2 24.0 - - + -
76A ILE* 5.5 0.4 - - + -
77A ILE* 4.1 22.9 - - + -
80A LEU* 4.0 21.3 - - + -
136A VAL* 4.5 4.5 - - + -
137A GLU* 3.2 11.9 - - - +
138A LEU* 3.6 20.4 - - + -
139A VAL* 5.8 0.4 - - - -
161A ARG* 3.6 4.0 - - - +
162A ILE* 3.0 41.7 + - + +
164A VAL* 4.3 8.3 - - + -
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Residues in contact with ARG 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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54A ILE* 1.3 82.1 - - - +
56A ILE* 1.3 65.5 + - - +
59A VAL 5.6 0.4 - - - +
135A GLU 3.9 0.3 - - - +
136A VAL* 3.3 7.1 - - - +
137A GLU* 3.0 59.5 + - + +
158A GLU* 5.4 7.1 - - - +
160A GLY* 3.2 34.0 - - - +
161A ARG* 3.6 33.0 - - - +
162A ILE* 5.1 2.5 - - - +
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Residues in contact with ILE 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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54A ILE* 4.2 16.6 - - + -
55A ARG* 1.3 84.0 - - - +
57A ASP* 1.3 71.0 + - + +
58A GLY 3.2 0.7 + - - -
59A VAL* 2.9 46.8 + - + +
66A VAL* 4.1 4.5 - - + -
73A VAL* 4.1 31.0 - - + -
76A ILE* 4.6 16.2 - - + -
134A LEU* 3.7 28.3 - - + -
135A GLU 3.5 7.2 - - - +
136A VAL* 3.7 16.8 - - + -
162A ILE* 5.2 4.6 - - + +
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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