Contacts of the strand formed by residues 312 - 321 (chain C) in PDB entry 2GD4
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 GLU 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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258C PHE 3.5 0.2 - - - +
259C ARG* 3.2 4.2 - - - +
260C TYR* 2.5 45.5 + - - +
261C ARG* 6.1 1.6 - - + -
310C GLU* 5.5 2.2 - - + -
311C LEU* 1.3 79.8 - - - +
313C GLU* 1.3 62.7 + - - +
314C MET* 3.5 26.4 + - + +
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Residues in contact with GLU 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LYS* 3.8 33.9 - - + +
258C PHE* 3.1 10.7 - - - +
259C ARG* 4.0 16.4 - - + +
312C GLU* 1.3 73.7 + - - +
314C MET* 1.3 64.7 + - - +
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Residues in contact with MET 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257C LYS* 2.8 28.8 - - - -
258C PHE 2.7 18.0 + - - +
260C TYR* 3.9 23.6 - - + +
312C GLU* 3.5 30.2 + - + +
313C GLU* 1.3 78.7 - - - +
315C MET* 1.3 65.3 + - - +
316C LEU* 3.4 5.4 + - + +
398C ASN* 5.1 5.2 - - + +
400C VAL* 3.9 26.7 - - + -
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Residues in contact with MET 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C GLU* 3.3 26.9 - - + +
256C GLY* 3.0 48.9 - - - +
257C LYS* 3.6 18.4 - - + +
314C MET* 1.3 72.8 - - - +
316C LEU* 1.3 60.3 + - - +
396C ASN* 3.6 45.3 - - + +
398C ASN 4.0 2.8 + - - +
399C ARG* 3.1 10.7 - - + +
400C VAL 3.1 18.2 + - - -
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Residues in contact with LEU 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255C GLU* 3.8 3.1 - - - -
256C GLY 3.2 21.0 + - - +
258C PHE* 3.4 37.0 - - + +
260C TYR* 3.2 50.3 - - + -
270C LEU* 3.8 12.1 - - + -
314C MET* 4.3 6.3 - - + +
315C MET* 1.3 75.3 - - - +
317C VAL* 1.3 65.0 + - - +
318C VAL* 3.7 15.9 + - + +
400C VAL* 2.7 27.1 - - + +
401C THR* 4.7 0.4 - - - -
402C PHE* 5.0 7.0 - - + -
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Residues in contact with VAL 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B GLU* 4.3 2.0 - - - +
253C TYR* 3.2 47.8 - - + +
254C GLN 3.8 4.5 - - - +
255C GLU* 3.5 21.5 - - + +
316C LEU* 1.3 73.6 - - - +
318C VAL* 1.3 56.8 + - - +
319C HIS* 4.1 1.8 - - - +
399C ARG* 3.5 28.3 - - + +
400C VAL 2.7 11.8 + - - +
401C THR* 3.3 21.3 - - + +
402C PHE* 2.7 33.3 + - - +
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229C PHE* 3.8 11.0 - - + -
252C MET 3.7 0.2 - - - +
253C TYR* 3.3 24.6 - - - -
254C GLN* 2.9 19.7 + - + +
258C PHE* 4.1 20.9 - - + -
270C LEU* 3.6 26.2 - - + -
272C LEU* 4.8 5.4 - - + -
283C LEU* 5.2 0.4 - - + -
316C LEU* 3.8 23.8 - - + +
317C VAL* 1.3 76.4 - - - +
319C HIS* 1.3 72.0 + - - +
320C MET* 3.7 12.5 + - + -
402C PHE* 3.4 11.2 - - + +
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Residues in contact with HIS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ARG* 4.7 6.4 + - - -
237C GLU* 4.4 13.8 + - - -
251C MET* 4.7 12.8 - - + -
252C MET 3.4 8.3 - - - +
253C TYR* 3.3 34.3 - + + -
317C VAL* 4.1 1.6 - - - +
318C VAL* 1.3 79.9 - - - +
320C MET* 1.3 59.5 + - - +
321C PRO* 4.8 0.2 - - - -
401C THR* 3.7 27.8 - - + +
402C PHE 2.7 9.2 + - - +
403C LYS* 3.4 25.6 - - + +
404C ALA* 2.8 32.7 + - - +
405C ASN* 5.5 2.0 - - + +
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Residues in contact with MET 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225C TRP* 4.1 14.6 - - - -
229C PHE* 4.4 9.9 - - + -
251C MET* 4.0 2.7 - - - -
252C MET* 2.5 68.8 + - + +
272C LEU* 3.6 22.2 - - + -
281C MET* 4.6 4.0 - - - +
283C LEU* 3.1 50.5 - - + -
318C VAL* 3.7 7.2 + - + -
319C HIS* 1.3 75.3 - - - +
321C PRO* 1.3 71.4 - - + +
323C PHE* 5.4 4.3 - - + -
375C VAL* 4.8 4.7 - - - -
404C ALA* 4.9 2.5 - - + -
408C PHE* 5.1 7.6 - - + -
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Residues in contact with PRO 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C PHE* 4.2 8.5 - - + -
249C ALA* 4.8 0.2 - - + -
250C SER 3.0 15.3 - - - +
251C MET* 3.6 17.9 - - + -
252C MET* 3.3 14.1 - - - +
320C MET* 1.3 96.7 - - + +
322C ARG* 1.3 60.5 + - - +
323C PHE* 3.7 15.6 - - + -
375C VAL* 4.2 1.6 - - - +
404C ALA* 3.8 16.8 - - + +
408C PHE* 4.0 23.8 - - + -
426C VAL* 4.8 0.2 - - + -
429C PRO* 4.3 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