Contacts of the strand formed by residues 122 - 126 (chain B) in PDB entry 5H1C
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 ILE 122 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B SER* 1.3 75.7 - - - +
123B THR* 1.3 64.1 + - - +
249B LEU* 4.3 10.3 - - + +
252B LEU* 4.0 24.2 - - + +
253B LEU* 3.9 31.9 - - + -
256B ALA* 5.2 0.4 - - + -
263B VAL* 3.6 17.9 - - + -
265B ILE* 2.9 37.5 - - + -
295B ALA* 5.0 10.5 - - + +
296B SER* 4.2 21.6 - - - +
297B THR* 2.8 28.4 + - + +
298B THR* 3.2 12.1 + - - -
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Residues in contact with THR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ILE* 3.7 36.9 - - + +
118B GLU 5.5 0.7 - - - +
121B SER* 5.1 5.8 - - - +
122B ILE* 1.3 76.4 - - - +
124B GLU* 1.3 65.9 + - - +
125B MET* 5.6 2.2 - - - -
263B VAL 2.9 21.8 + - - +
264B VAL* 3.2 22.4 - - - +
265B ILE* 2.8 32.0 + - - +
298B THR* 3.2 24.7 - - + +
300B LEU* 5.8 4.9 - - - -
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Residues in contact with GLU 124 (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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123B THR* 1.3 77.0 + - - +
125B MET* 1.3 65.0 + - - +
126B PHE* 3.8 3.6 - - + -
265B ILE* 3.1 9.4 - - - +
267B ASN* 2.5 39.4 + - - +
292B ILE* 2.7 22.6 - - - +
296B SER* 3.0 24.0 - - - -
298B THR* 4.3 3.0 + - - -
299B ARG* 2.5 55.4 + - - +
300B LEU* 2.9 35.5 + - - +
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Residues in contact with MET 125 (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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117B ILE* 5.3 5.6 - - + -
123B THR* 5.3 1.3 - - - +
124B GLU* 1.3 85.9 - - - +
126B PHE* 1.3 66.5 + - - +
133B LYS* 3.8 21.5 - - + +
136B ILE* 4.0 36.3 - - + -
137B CYS* 5.1 2.0 - - - -
140B LEU* 5.2 2.7 - - + -
264B VAL* 4.3 20.2 - - + -
265B ILE 2.8 15.0 + - - +
266B THR* 3.2 34.5 - - + +
267B ASN* 3.1 26.5 + - - +
300B LEU* 4.5 21.1 - - + -
302B LEU* 4.8 7.4 - - + -
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Residues in contact with PHE 126 (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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129A PHE* 5.9 2.7 - + - -
130A ARG* 6.2 0.7 - - - -
124B GLU* 3.8 8.3 - - + -
125B MET* 1.3 79.7 - - - +
127B GLY* 1.3 57.2 + - - +
131B THR* 5.1 0.4 - - - -
133B LYS* 5.5 0.4 - - - -
267B ASN* 4.2 2.9 - - + -
269B VAL* 5.2 4.9 - - + -
284B LYS* 6.1 0.2 - - + -
285B LYS* 4.5 4.0 - - - -
286B PRO* 2.3 61.5 - - + -
299B ARG* 2.7 37.7 - - - -
300B LEU 2.8 25.5 + - - +
301B TYR* 3.3 27.8 - + + -
302B LEU* 2.6 37.9 + - - +
315B TYR* 4.1 19.3 - + - -
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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