Contacts of the strand formed by residues 268 - 276 (chain I) in PDB entry 1F1H
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 MET 268 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128I PRO* 3.8 25.8 - - + -
129I GLU 3.4 4.0 - - - -
130I PRO* 3.8 25.4 - - + -
235I ILE* 4.2 14.4 - - + -
239I LYS* 6.4 0.2 - - - -
267I GLY* 1.3 75.6 - - - +
269I HIS* 1.3 66.2 + - - +
270I CYS* 3.4 5.8 + - - -
321I ARG* 4.4 0.2 - - - +
361I PRO* 2.7 34.6 + - + +
362I ASP 3.6 29.6 - - - +
363I PRO* 3.7 11.7 - - + +
365I ALA* 4.3 17.9 - - + +
367I PRO* 5.2 4.5 - - + -
370I CYS* 4.9 1.6 - - - -
371I PHE* 4.3 21.1 - - + -
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Residues in contact with HIS 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50H ASP* 5.7 4.3 - - - -
127I GLY 3.7 1.0 - - - +
128I PRO* 3.1 4.3 - - - +
129I GLU* 2.7 47.4 + - + +
131I GLU* 5.7 7.7 + - - -
267I GLY* 3.9 2.3 - - - -
268I MET* 1.3 76.8 - - - +
270I CYS* 1.3 59.6 + - - +
271I HIS 4.0 0.7 - - - -
321I ARG* 4.5 9.9 + - - -
329I PRO* 5.6 1.0 - - - +
357I GLU* 3.0 16.0 + - + +
358I VAL 3.5 6.7 - - - +
359I ARG* 3.4 63.0 + - + +
470I MN 2.3 32.2 + - - -
1479I ADP 4.8 2.4 + - - -
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Residues in contact with CYS 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126I PHE* 4.7 11.0 - - + -
127I GLY 4.0 2.9 - - - -
128I PRO* 4.4 7.6 - - + -
268I MET* 3.4 18.4 - - - -
269I HIS* 1.3 76.0 - - - +
271I HIS* 1.3 61.7 + - - +
272I MET* 3.7 8.9 + - + +
356I ILE 3.6 1.4 - - - +
357I GLU* 3.4 2.3 - - - -
358I VAL* 2.8 40.2 + - + +
361I PRO* 4.3 14.4 - - + -
370I CYS* 5.0 0.4 - - - -
371I PHE* 4.0 27.4 - - - -
374I LEU* 4.5 18.2 - - + -
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Residues in contact with HIS 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125I LEU 3.7 0.2 - - - +
126I PHE* 3.5 2.1 - - - +
127I GLY 2.9 46.4 + - - +
129I GLU* 3.1 21.6 + - + -
269I HIS* 5.1 0.2 - - + -
270I CYS* 1.3 72.6 - - - +
272I MET* 1.3 65.0 + - - +
344I ARG* 4.8 3.4 - - - -
346I PRO* 4.1 9.8 - - + +
355I ARG* 2.9 29.8 + - - -
356I ILE 3.2 5.8 + - - +
357I GLU* 3.0 43.2 + - + +
1479I ADP 3.2 48.1 + - + +
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Residues in contact with MET 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I VAL* 6.0 0.9 - - + -
125I LEU 3.2 8.5 - - - +
126I PHE* 3.5 42.6 - - + -
270I CYS* 3.9 10.8 - - + +
271I HIS* 1.3 80.5 - - - +
273I SER* 1.3 60.8 + - - +
282I PHE* 4.0 2.4 - - - -
297I TYR* 3.6 27.1 - - + +
301I VAL* 5.2 0.4 - - + -
355I ARG* 3.0 22.1 - - - +
356I ILE* 2.8 35.1 + - + +
358I VAL* 3.2 35.9 - - + -
374I LEU* 3.9 18.4 - - + -
1479I ADP 4.5 2.4 + - - -
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Residues in contact with SER 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124I VAL* 3.9 3.1 - - - +
125I LEU* 2.9 40.1 + - - +
272I MET* 1.3 79.4 - - - +
274I LEU* 1.3 66.7 + - - +
275I ALA* 5.7 0.2 - - - +
280I ASN* 3.9 11.6 + - - -
282I PHE* 3.8 12.3 - - - -
297I TYR* 6.2 0.2 - - - -
354I ARG 3.7 17.9 - - - -
355I ARG* 3.9 0.4 - - - -
1479I ADP 2.9 30.2 + - - -
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Residues in contact with LEU 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115I LEU* 3.9 16.8 - - + -
120I ILE* 4.8 3.6 - - + -
121I ALA* 4.0 13.9 - - + -
123I THR 3.7 9.4 - - - +
124I VAL* 3.3 32.3 - - + -
125I LEU* 5.8 0.2 - - - -
273I SER* 1.3 76.0 + - - +
275I ALA* 1.3 62.8 + - - +
280I ASN* 3.4 8.0 - - - +
281I LEU* 3.1 26.7 + - + +
282I PHE* 3.5 30.4 - - + -
293I GLN* 5.1 1.8 - - - +
297I TYR* 3.8 22.7 - - + -
375I LEU* 4.4 3.8 - - + -
379I LEU* 4.3 10.3 - - + -
382I ILE* 4.1 14.8 - - + -
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Residues in contact with ALA 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ALA* 3.2 4.5 - - - +
122I ASP* 2.8 30.5 + - - +
123I THR* 3.1 24.6 + - - +
125I LEU* 5.0 12.6 - - + -
273I SER* 5.7 0.2 - - - +
274I LEU* 1.3 78.3 - - - +
276I LYS* 1.3 60.7 + - - +
278I GLY* 5.2 5.2 - - - +
279I THR 3.2 19.1 - - - +
280I ASN* 4.7 1.8 - - - -
281I LEU* 4.0 2.2 - - - -
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Residues in contact with LYS 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119I GLY* 2.9 35.9 + - - +
120I ILE 4.6 3.8 - - - +
121I ALA* 4.3 11.0 - - - +
122I ASP* 3.2 17.5 + - - +
275I ALA* 1.3 75.3 - - - +
277I ASN* 1.3 88.9 + - - +
278I GLY 3.2 0.7 - - - -
279I THR* 2.8 25.3 + - - -
281I LEU* 3.5 18.6 - - + +
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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