Contacts of the strand formed by residues 114 - 119 (chain B) in PDB entry 1UMD
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 114 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PRO 3.0 10.9 + - - +
78B VAL* 3.4 9.1 - - + -
79B ALA* 2.7 33.8 + - - +
113B LEU* 1.3 81.9 - - - +
115B VAL* 1.3 63.3 + - - +
116B ARG* 3.9 5.8 - - + -
158B LEU* 4.3 15.7 - - + -
161B ALA* 3.6 39.3 - - + +
162B ILE* 3.9 14.6 - - + +
168B VAL* 3.4 11.2 - - + +
170B PHE* 4.1 20.9 - - + -
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Residues in contact with VAL 115 (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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64B VAL* 4.8 11.7 - - + -
67B ALA* 6.0 0.4 - - + -
79B ALA* 3.4 13.7 - - + +
81B ILE* 3.6 32.3 - - + -
87B ILE* 4.6 6.1 - - + -
94B LEU* 4.6 17.5 - - + -
113B LEU* 3.5 25.1 - - + -
114B VAL* 1.3 73.0 - - - +
116B ARG* 1.3 58.9 + - - +
117B MET* 3.8 14.0 - - + +
168B VAL 2.9 12.8 + - - +
169B VAL* 3.5 11.6 - - + +
170B PHE 2.8 25.2 + - - +
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Residues in contact with ARG 116 (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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14B LEU* 4.6 5.2 - - - +
26B VAL* 5.5 2.4 - - - +
40B VAL* 3.3 34.1 - - - +
41B THR* 4.3 9.9 - - - +
78B VAL* 3.7 29.1 - - + +
79B ALA 2.7 11.9 + - - +
80B GLU* 2.8 41.4 + - - +
81B ILE* 2.9 27.2 + - - +
114B VAL* 4.3 4.0 - - + -
115B VAL* 1.3 73.9 - - - +
117B MET* 1.3 62.5 + - - +
118B PRO* 5.3 2.8 - - - +
158B LEU* 4.3 27.1 - - + +
170B PHE* 3.4 8.5 - - + -
172B GLU* 2.7 38.0 + - - +
177B TYR* 4.0 3.0 + - - -
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Residues in contact with MET 117 (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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81B ILE* 3.5 13.5 - - + +
84B ALA* 3.6 35.4 - - + +
87B ILE* 3.9 20.9 - - + -
94B LEU* 5.7 0.4 - - + -
115B VAL* 3.8 23.1 - - + +
116B ARG* 1.3 77.7 - - - +
118B PRO* 1.3 70.4 - - + +
137B PHE* 3.8 24.7 - - + -
169B VAL* 3.7 22.4 - - + -
170B PHE 3.0 12.2 + - - +
171B LEU* 3.4 12.0 - - + +
172B GLU* 2.9 28.8 + - - -
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Residues in contact with PRO 118 (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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38B PHE* 3.9 15.3 - - + -
80B GLU* 5.1 8.3 - - + +
81B ILE 3.3 7.9 - - - +
82B GLN* 3.2 28.0 - - - +
83B PHE* 3.9 1.3 - - - -
84B ALA* 2.8 27.0 + - - +
116B ARG* 5.3 2.2 - - - +
117B MET* 1.3 84.8 - - + +
119B SER* 1.3 58.3 + - - +
172B GLU* 3.1 12.3 - - - +
174B LYS* 3.9 19.2 - - + -
177B TYR* 3.2 30.1 - - + +
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Residues in contact with SER 119 (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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84B ALA* 3.8 11.0 - - - -
117B MET 4.4 1.3 - - - -
118B PRO* 1.3 75.9 - - - +
120B GLY* 1.3 68.7 + - - +
131B GLN 3.6 12.8 - - - -
132B SER* 4.7 3.7 + - - -
134B GLU* 5.3 0.3 + - - -
171B LEU* 3.7 31.7 - - - +
172B GLU 2.8 7.7 + - - -
173B PRO* 3.2 16.6 - - - +
174B LYS* 2.9 31.0 + - - +
175B ARG 4.7 0.5 + - - -
212B THR* 4.7 1.4 + - - -
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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