Contacts of the strand formed by residues 310 - 318 (chain A) in PDB entry 1XPM
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 VAL 310 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLU* 3.8 13.0 + - + +
112A TYR* 3.6 41.0 - - + +
177A ALA* 4.7 0.7 - - + -
178A TYR 3.4 5.4 - - - +
179A THR* 3.6 21.8 - - - +
208A SER* 4.1 3.6 - - - -
305A TYR* 3.5 2.9 - - - -
306A GLY 2.8 31.5 + - - -
309A SER* 1.3 81.4 - - - +
311A GLY* 1.3 65.6 + - - +
90B VAL* 3.9 12.3 - - + -
102B ALA 4.4 4.5 - - - +
103B ARG* 4.6 0.2 - - - -
104B CYS* 3.7 24.7 - - + +
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Residues in contact with GLY 311 (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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112A TYR* 4.5 0.9 - - - -
177A ALA* 3.1 5.7 - - - +
178A TYR 2.8 32.5 + - - -
208A SER* 3.3 19.3 + - - -
212A SER* 3.7 7.4 - - - -
303A PHE* 3.9 4.5 - - - -
304A SER 3.1 10.5 - - - -
310A VAL* 1.3 78.1 - - - +
312A GLU* 1.3 61.5 + - - +
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Residues in contact with GLU 312 (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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112A TYR* 2.6 39.9 + - + -
115A THR* 3.6 23.2 - - + +
119A GLN* 3.6 3.6 - - - +
175A ALA* 3.4 11.8 - - - +
176A VAL 3.3 18.8 - - - +
177A ALA* 3.8 2.4 - - - +
212A SER* 4.3 1.6 - - - -
302A LEU 3.6 1.0 - - - +
303A PHE* 3.3 10.2 - - - -
304A SER* 2.9 32.9 + - - +
311A GLY* 1.3 75.7 - - - +
313A PHE* 1.3 69.0 + - - +
314A TYR* 4.1 4.4 + - + -
103B ARG* 2.8 38.6 + - - +
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Residues in contact with PHE 313 (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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175A ALA* 3.4 1.2 - - - -
176A VAL* 3.0 30.5 + - - +
209A PHE* 4.1 20.0 - + - -
212A SER* 4.2 23.7 - - - +
213A TRP* 3.5 42.2 - + - -
216A TYR* 3.5 35.1 - + + -
227A PHE* 3.9 9.9 - + - -
230A LEU* 4.3 13.0 - - + -
301A GLY* 3.8 19.5 - - - -
302A LEU 3.2 14.4 - - - -
303A PHE* 4.2 13.0 - + + -
312A GLU* 1.3 74.4 - - - +
314A TYR* 1.3 74.3 + - - +
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Residues in contact with TYR 314 (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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115A THR* 3.7 22.0 - - + -
118A ILE* 3.6 6.4 - - + +
119A GLN* 3.3 23.3 - - - +
171A LEU* 3.9 17.4 - - + +
172A ASN 5.5 1.1 - - - +
174A ASP* 3.8 7.2 - - - +
175A ALA* 3.7 20.9 - - + +
216A TYR* 4.2 2.5 - - - -
281A LEU* 4.4 3.5 - - + +
282A TYR* 2.7 34.8 + - - -
301A GLY* 3.7 1.7 - - - -
302A LEU* 2.8 69.2 + - + +
304A SER* 4.9 0.7 - - - -
312A GLU* 4.1 14.4 - - + -
313A PHE* 1.3 85.4 - - - +
315A SER* 1.3 72.3 + - - +
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Residues in contact with SER 315 (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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171A LEU* 4.2 0.5 - - - -
172A ASN* 2.8 37.2 + - - +
174A ASP* 2.6 31.3 + - - +
216A TYR* 3.5 11.3 + - - -
222A LYS* 5.5 1.6 - - - -
227A PHE* 3.8 5.6 - - - -
299A THR* 3.6 14.2 - - - +
300A ILE 3.2 13.2 - - - -
302A LEU* 4.4 0.4 - - - -
314A TYR* 1.3 86.5 - - - +
316A ALA* 1.3 63.0 + - - +
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Residues in contact with ALA 316 (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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169A LEU* 3.8 27.2 - - + +
170A ALA 3.2 13.9 - - - +
171A LEU* 4.3 13.5 - - + -
172A ASN* 3.6 1.6 - - - +
298A GLU 4.1 0.2 - - - +
299A THR* 3.3 3.5 - - - +
300A ILE* 2.9 31.6 + - + +
302A LEU* 4.1 15.9 - - + -
314A TYR* 5.1 0.2 - - + -
315A SER* 1.3 76.5 - - - +
317A THR* 1.3 64.4 + - - +
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Residues in contact with THR 317 (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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169A LEU* 3.5 4.7 - - - -
170A ALA* 2.9 39.6 + - - +
172A ASN* 3.1 24.0 + - - -
297A GLY* 3.5 32.3 - - - +
298A GLU 3.5 4.5 - - - +
299A THR* 3.4 11.6 + - - +
316A ALA* 1.3 72.3 - - - +
318A LEU* 1.3 73.2 + - - +
319A VAL* 3.5 0.7 + - - +
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Residues in contact with LEU 318 (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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168A ILE 3.7 9.0 - - - +
169A LEU* 3.7 13.9 - - + -
289A LEU* 3.6 28.9 - - + -
294A LEU* 3.2 43.5 - - + -
295A GLN 3.5 22.7 - - - +
296A ALA* 4.0 4.0 - - - -
297A GLY* 2.9 25.2 + - - -
298A GLU* 3.0 18.6 + - + +
300A ILE* 4.6 4.9 - - + -
317A THR* 1.3 74.9 - - - +
319A VAL* 1.3 61.1 + - - +
320A GLU 4.0 0.3 + - - -
322A TYR* 3.9 24.5 - - + -
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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