Contacts of the strand formed by residues 2100 - 2104 (chain A) in PDB entry 5G1N
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 SER2100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2073A MET 2.9 7.1 + - - -
2074A THR* 2.4 32.7 + - - -
2075A ILE* 2.9 27.0 + - - +
2099A VAL* 1.3 76.0 - - - +
2101A LEU* 1.3 64.2 + - - +
2102A ARG* 5.5 0.7 - - - -
2124A THR* 4.1 1.3 - - - -
2125A LYS* 4.0 36.1 + - - -
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Residues in contact with LEU2101 (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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2075A ILE* 3.7 7.6 - - + +
2077A MET* 3.5 30.1 - - + -
2091A ALA* 4.3 13.9 - - + +
2094A LEU* 4.0 16.4 - - + -
2095A THR* 5.3 0.7 - - + -
2099A VAL* 5.9 0.9 - - + -
2100A SER* 1.3 75.8 - - - +
2102A ARG* 1.3 62.9 + - - +
2103A TYR* 3.4 42.4 - - + +
2119A VAL* 3.6 24.9 - - + -
2124A THR* 3.9 15.7 - - + -
2125A LYS* 2.7 19.3 + - - +
2126A GLN* 4.2 1.8 - - - -
2127A GLU 3.1 22.0 + - - -
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Residues in contact with ARG2102 (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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2074A THR* 3.5 23.2 - - + +
2075A ILE 3.0 7.6 + - - +
2076A THR* 3.2 21.8 - - + +
2077A MET 2.9 26.5 + - - -
2100A SER* 5.5 0.9 - - - -
2101A LEU* 1.3 78.5 - - - +
2103A TYR* 1.3 65.8 + - - +
2104A VAL 4.2 0.2 - - - -
2127A GLU* 3.3 8.7 - - + +
2129A PHE* 3.2 43.5 - - + -
2134A GLU 4.6 1.2 + - - -
2135A ALA* 2.7 38.6 + - - +
2137A PRO* 5.4 0.2 - - - +
2138A ASP* 3.6 37.9 + - - +
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Residues in contact with TYR2103 (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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2077A MET* 3.5 12.3 - - + -
2081A LEU* 3.5 17.0 - - + -
2091A ALA* 4.2 7.6 - - - +
2101A LEU* 3.4 49.0 - - + +
2102A ARG* 1.3 79.0 - - - +
2104A VAL* 1.3 62.2 + - - +
2111A MET* 3.9 34.6 - - + +
2116A ARG* 4.2 16.4 - - + -
2119A VAL* 4.3 1.9 - - - +
2126A GLN* 2.7 40.8 + - + -
2127A GLU 2.8 14.9 + - - +
2128A GLU* 2.9 32.6 - - + +
2129A PHE* 3.0 12.5 + - - -
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Residues in contact with VAL2104 (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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2076A THR* 3.9 23.1 - - + -
2077A MET 3.1 7.7 + - - +
2078A VAL* 3.3 20.1 - - + -
2079A GLY 2.8 28.7 + - - +
2081A LEU* 4.1 1.2 - - - +
2102A ARG 4.2 0.2 - - - -
2103A TYR* 1.3 74.2 - - - +
2105A ALA* 1.3 63.3 + - - +
2128A GLU* 3.4 2.2 - - - -
2129A PHE* 3.5 32.1 - - + +
2130A GLU 4.2 0.7 - - - -
2131A SER* 3.8 31.6 - - - +
2132A ILE* 4.2 1.6 - - - +
2135A ALA* 4.1 1.6 - - + -
2165A PHE* 3.8 19.5 - - + -
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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