Contacts of the strand formed by residues 299 - 308 (chain A) in PDB entry 2IFG
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 TRP 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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293A ALA* 3.8 22.9 - - + -
294A VAL* 3.4 33.4 - - - -
295A GLU* 3.2 46.2 + - + +
298A HIS* 1.3 78.0 - - - +
300A CYS* 1.3 61.5 + - - +
347A ARG* 3.6 3.5 - - - -
348A LEU* 2.8 50.1 + - + +
350A GLN* 5.3 1.8 - - - -
351A PRO* 3.5 27.1 + - + +
377A ALA 4.3 12.1 - - - -
378A PHE* 3.9 39.9 + + + +
59E ARG* 5.9 3.1 - - - -
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Residues in contact with CYS 300 (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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293A ALA* 4.3 1.1 - - - -
294A VAL* 2.7 45.1 + - - +
296A MET* 4.6 11.4 - - + -
298A HIS* 4.8 2.7 - - + +
299A TRP* 1.3 77.1 - - - +
301A ILE* 1.3 60.9 + - - +
302A PRO* 3.1 23.6 - - - +
345A CYS* 2.0 49.8 - - + -
346A LEU 3.3 4.7 - - - -
347A ARG* 5.0 3.1 - - + -
348A LEU* 4.4 0.2 - - - -
6E ILE* 4.6 2.9 - - + -
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Residues in contact with ILE 301 (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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290A LEU* 4.3 5.8 - - + -
291A HIS 3.8 10.3 - - - +
293A ALA* 4.1 17.5 - - + +
300A CYS* 1.3 73.8 - - - +
302A PRO* 1.3 64.5 - - - +
303A PHE* 3.6 2.8 + - - -
315A TRP* 4.0 13.6 - - + -
345A CYS* 3.3 1.4 - - - -
346A LEU* 2.9 58.8 + - + +
348A LEU* 4.0 13.2 - - + -
359A TYR* 3.7 30.5 - - + -
374A ILE* 3.8 25.1 - - + -
376A ALA* 4.7 6.5 - - + -
378A PHE* 4.9 2.0 - - + -
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Residues in contact with PRO 302 (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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290A LEU* 3.5 4.5 - - - +
291A HIS* 2.9 66.3 + - + +
292A THR 4.0 8.3 - - - +
294A VAL* 3.9 14.1 - - + -
300A CYS* 3.1 22.9 - - - +
301A ILE* 1.3 83.8 - - - +
303A PHE* 1.3 59.2 + - - +
344A GLY 3.4 7.4 - - - +
4E HIS* 4.0 19.7 - - + +
6E ILE* 4.5 7.6 - - + -
7E PHE* 5.2 5.2 - - + -
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Residues in contact with PHE 303 (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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289A GLN 3.4 7.6 - - - +
290A LEU* 4.0 4.9 - - + -
291A HIS* 4.7 0.4 - - - -
301A ILE 4.3 1.3 - - - +
302A PRO* 1.3 76.0 - - - +
304A SER* 1.3 70.9 + - - +
305A VAL* 4.2 9.0 - - + -
313A LEU* 3.5 24.2 - - + -
315A TRP* 4.3 11.0 - + + -
330A THR* 3.8 18.2 - - + -
331A GLU 3.8 4.0 - - - -
332A PHE* 3.9 22.9 - + - -
342A ARG 4.4 1.1 - - - -
343A HIS* 3.4 3.1 - - - -
344A GLY* 2.9 58.7 + - - -
345A CYS* 3.2 28.7 - - - -
361A LEU* 3.5 29.8 - - + -
4E HIS* 3.1 9.3 + - - -
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Residues in contact with SER 304 (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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288A VAL* 3.5 3.3 - - - +
289A GLN* 2.9 53.8 + - - +
291A HIS* 4.0 5.0 + - - -
303A PHE* 1.3 76.1 + - - +
305A VAL* 1.3 61.5 + - - +
341A VAL* 4.9 3.8 - - - -
342A ARG 3.3 6.7 - - - -
343A HIS* 3.2 27.2 + - - -
4E HIS* 3.5 14.4 + - - -
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Residues in contact with VAL 305 (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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287A SER 3.1 17.0 - - - +
288A VAL* 3.5 4.7 - - + -
303A PHE* 4.2 15.5 - - + -
304A SER* 1.3 76.7 - - - +
306A ASP* 1.3 61.9 + - - +
311A PRO* 3.3 32.1 - - + +
313A LEU* 4.2 12.1 - - + -
332A PHE* 4.7 4.3 - - + -
340A THR 4.5 0.5 - - - +
341A VAL* 3.5 4.2 - - - +
342A ARG* 2.9 53.1 + - + +
363A ALA* 3.5 19.3 - - + -
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Residues in contact with ASP 306 (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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284A PHE* 2.9 16.3 - - + -
286A ALA* 3.3 4.3 - - - -
287A SER* 2.9 42.7 + - - +
305A VAL* 1.3 74.1 - - - +
307A GLY* 1.3 74.2 + - - +
311A PRO* 3.6 14.9 - - - +
340A THR* 2.8 31.7 + - - -
341A VAL* 3.6 22.7 + - + +
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Residues in contact with GLY 307 (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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284A PHE* 3.4 21.0 - - - -
285A PRO 3.9 6.3 - - - -
286A ALA* 4.1 4.7 - - - -
306A ASP* 1.3 92.2 + - - +
308A GLN* 1.3 63.3 + - - +
309A PRO 3.3 8.5 - - - +
310A ALA* 3.7 10.6 - - - +
311A PRO* 4.1 3.8 - - - +
340A THR* 4.3 10.0 - - - +
365A ASN* 5.1 0.2 - - - -
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Residues in contact with GLN 308 (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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259A ASN* 4.3 3.1 - - - +
260A ARG* 4.8 1.2 - - - +
281A ASN* 2.7 34.4 + - - +
282A VAL 3.0 24.2 - - - +
283A SER* 2.9 23.6 - - - -
284A PHE* 3.0 39.5 + - + +
307A GLY* 1.3 75.1 + - - +
309A PRO* 1.3 79.9 + - - +
310A ALA* 3.7 1.8 - - - +
340A THR* 4.7 5.8 - - + +
365A ASN* 4.2 0.4 - - - -
367A PHE* 3.8 0.7 - - - -
1G NAG 3.1 28.6 + - - +
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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