Contacts of the strand formed by residues 2210 - 2220 (chain B) in PDB entry 2H7C
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 GLY2210 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2132B ARG* 3.0 18.1 + - - -
2133B LEU 3.5 6.7 - - - -
2135B VAL* 3.9 7.6 - - - -
2164B VAL* 3.9 13.2 - - - -
2205B ILE* 3.0 16.5 + - - -
2206B ALA* 3.2 15.4 + - - -
2208B PHE 3.3 1.6 - - - -
2209B GLY* 1.3 81.2 - - - +
2211B ASN* 1.3 60.1 + - - -
2212B PRO* 3.4 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN2211 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2132B ARG* 3.4 33.0 + - + +
2133B LEU 2.8 19.6 + - - +
2135B VAL* 3.7 6.4 - - - +
2205B ILE* 4.1 2.0 - - - -
2210B GLY* 1.3 72.7 - - - -
2212B PRO* 1.3 63.7 - - - +
2213B GLY* 3.0 21.9 + - - -
2214B SER* 3.0 48.0 + - - +
2215B VAL* 4.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO2212 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2132B ARG* 4.4 5.4 - - - +
2202B GLN* 2.7 64.9 + - - +
2205B ILE* 3.7 16.5 - - + -
2206B ALA* 4.3 12.8 - - + -
2210B GLY 3.4 10.1 - - - +
2211B ASN* 1.3 87.2 - - - +
2213B GLY* 1.3 55.8 + - - +
2214B SER 3.2 1.1 + - - -
2215B VAL* 3.5 3.6 - - + +
2241B HIS* 3.2 10.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2213 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2211B ASN* 3.0 15.3 + - - -
2212B PRO* 1.3 80.0 - - - +
2214B SER* 1.3 57.3 - - - +
2241B HIS* 3.3 28.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER2214 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2134B PRO* 3.8 12.1 - - - +
2135B VAL 2.9 23.7 + - - +
2211B ASN* 3.0 29.6 + - - +
2213B GLY* 1.3 79.8 - - - +
2215B VAL* 1.3 58.9 - - - +
2216B THR 4.1 0.2 + - - -
2241B HIS* 3.6 6.3 - - - -
2242B ARG* 4.1 7.3 + - - +
2504B ALA 3.4 21.9 + - - +
2505B ARG* 4.5 3.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL2215 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135B VAL* 3.4 8.1 - - + +
2137B VAL* 3.8 27.8 - - + -
2198B LEU* 4.2 8.5 - - + -
2201B VAL* 4.1 16.2 - - + -
2202B GLN* 3.5 25.4 - - - +
2211B ASN 4.0 6.3 - - - +
2212B PRO* 3.5 9.0 - - + +
2214B SER* 1.3 74.0 - - - +
2216B THR* 1.3 66.3 + - - +
2239B LEU 3.7 20.2 - - - +
2240B PHE* 3.5 3.9 - - + +
2241B HIS* 2.7 42.9 + - - +
2242B ARG* 3.4 2.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR2216 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2135B VAL 2.7 14.9 + - - -
2136B MET* 3.5 14.2 - - + -
2137B VAL* 2.8 29.3 + - - +
2214B SER 5.1 0.3 + - - -
2215B VAL* 1.3 73.4 - - - +
2217B ILE* 1.3 72.1 + - - +
2218B PHE* 4.8 1.1 - - + +
2242B ARG* 3.3 31.1 - - + +
2244B ILE* 4.3 22.9 - - + -
2503B PHE* 4.7 0.4 - - + -
2504B ALA* 3.2 34.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE2217 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2137B VAL* 3.4 9.9 - - + +
2139B ILE* 4.8 6.3 - - + -
2198B LEU* 3.5 34.8 - - + -
2215B VAL* 4.6 0.9 - - + -
2216B THR* 1.3 77.4 - - - +
2218B PHE* 1.3 62.2 + - - +
2227B VAL* 4.0 24.0 - - + +
2230B LEU* 4.2 21.1 - - + -
2240B PHE* 3.6 44.9 - - + -
2242B ARG 3.0 13.4 + - - +
2243B ALA* 3.3 5.6 - - + -
2244B ILE 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE2218 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2136B MET* 3.6 40.8 - - + -
2137B VAL 3.0 20.2 + - - +
2138B TRP* 3.2 59.9 - + + -
2139B ILE* 2.9 23.7 + - - +
2157B LEU* 4.2 11.0 - - + -
2165B VAL* 4.9 2.7 - - + -
2216B THR* 4.4 1.8 - - + -
2217B ILE* 1.3 77.6 - - - +
2219B GLY* 1.3 56.7 + - - +
2227B VAL* 3.8 5.1 - - - +
2244B ILE* 3.2 30.3 - - + -
2246B GLU* 3.7 10.1 - - - +
2475B VAL* 4.0 19.5 - - + -
2476B PHE* 4.0 9.4 - + - -
2500B TRP* 4.0 9.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY2219 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2138B TRP* 3.5 11.4 - - - -
2139B ILE 3.1 17.0 - - - -
2218B PHE* 1.3 75.7 - - - +
2220B GLU* 1.3 59.7 + - - -
2223B GLY 3.7 9.0 - - - -
2224B GLY* 3.3 12.0 - - - -
2227B VAL* 3.7 2.4 - - - +
2244B ILE 3.2 6.3 + - - +
2246B GLU* 2.9 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU2220 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2101B PHE* 3.9 15.2 - - - -
2138B TRP* 3.5 23.9 - - + -
2139B ILE 3.6 2.6 + - - -
2141B GLY* 3.2 14.2 + - - -
2152B TYR* 5.4 0.5 + - - -
2219B GLY* 1.3 74.1 - - - +
2221B SER* 1.3 72.7 + - - +
2223B GLY 2.8 20.6 + - - -
2224B GLY 3.4 0.8 - - - +
2246B GLU* 3.1 10.8 - - + +
2247B SER* 4.3 1.1 - - - -
2468B HIS* 3.1 29.3 + - - -
2469B GLY* 3.5 20.3 + - - -
2471B GLU* 3.1 27.1 - - - +
2472B LEU* 3.8 12.7 - - + +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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