Contacts of the strand formed by residues 320 - 330 (chain 0) in PDB entry 6FF7
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 320 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3120 GLU* 6.3 1.1 - - + -
3130 TYR 3.2 11.4 - - - +
3140 THR* 5.0 3.6 - - - -
3180 GLY 3.5 6.3 + - - +
3190 THR* 1.4 73.6 - - - +
3210 GLY* 1.4 58.7 + - - +
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Residues in contact with GLY 321 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3120 GLU* 3.2 7.9 - - - +
3130 TYR* 2.8 35.6 + - - +
3200 VAL* 1.4 76.2 - - - +
3220 ARG* 1.4 58.3 + - - -
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Residues in contact with ARG 322 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3100 LEU* 4.7 15.0 - - + -
3110 VAL 3.4 8.3 - - - +
3120 GLU* 4.6 0.9 - - - +
3210 GLY* 1.4 70.3 - - - -
3230 ARG* 1.3 58.2 + - - +
3240 VAL 4.3 0.5 + - - -
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Residues in contact with ARG 323 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3090 ARG 3.3 2.9 - - - +
3100 LEU* 3.5 3.5 - - - -
3110 VAL* 2.8 39.1 + - + +
3130 TYR* 4.2 18.4 - - + -
3210 GLY 3.9 0.2 + - - -
3220 ARG* 1.3 73.1 - - - +
3240 VAL* 1.3 66.9 + - - +
3250 LYS* 3.4 4.0 + - + +
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Residues in contact with VAL 324 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2540 ILE 5.6 1.3 - - - +
2550 PRO* 5.2 5.6 - - + -
2560 LYS* 4.6 25.6 - - + +
2570 LYS* 5.6 3.6 - - + +
3080 TYR* 5.9 3.8 - - + -
3090 ARG 3.4 7.9 - - - +
3100 LEU* 4.9 1.1 - - - +
3220 ARG 4.3 0.6 + - - -
3230 ARG* 1.3 71.4 - - - +
3250 LYS* 1.3 59.3 + - - +
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Residues in contact with LYS 325 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3070 GLN 3.8 0.9 - - - +
3080 TYR* 3.6 2.8 - - - +
3090 ARG* 2.9 37.7 + - + +
3110 VAL* 5.6 7.9 - - + -
3230 ARG* 3.4 6.2 + - + +
3240 VAL* 1.3 73.6 - - - +
3260 PRO* 1.3 62.0 - - - +
3270 TYR* 4.0 1.4 + - + +
3510 GLU* 6.1 4.0 - - + -
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Residues in contact with PRO 326 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3070 GLN 3.4 9.0 - - - +
3080 TYR* 4.3 5.4 - - + -
3240 VAL 4.3 0.4 - - - -
3250 LYS* 1.3 76.1 - - - +
3270 TYR* 1.3 60.4 + - - +
3510 GLU* 4.0 4.3 - - - +
3520 LEU* 3.1 38.1 + - + +
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Residues in contact with TYR 327 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3050 VAL 3.7 0.5 - - - +
3060 PHE* 3.6 4.2 - - - +
3070 GLN* 2.8 42.9 + - + +
3090 ARG* 6.6 0.4 - - + -
3250 LYS* 5.2 0.9 - - + +
3260 PRO* 1.3 75.5 - - - +
3280 ILE* 1.3 60.6 + - - +
3490 TYR* 3.7 26.2 - - + +
3500 TYR 3.1 14.6 - - - +
3510 GLU* 4.9 1.3 - - - -
3520 LEU* 4.3 3.8 - - - +
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Residues in contact with ILE 328 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3040 ALA* 5.7 5.4 - - + -
3050 VAL 3.4 8.3 - - - +
3060 PHE* 5.3 2.0 - - - -
3270 TYR* 1.3 73.9 - - - +
3290 ILE* 1.3 60.6 + - - +
3480 ARG 3.5 1.4 - - - +
3490 TYR* 4.3 0.7 - - - -
3500 TYR* 2.7 45.1 + - + +
3520 LEU* 5.3 8.1 - - + -
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Residues in contact with ILE 329 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3040 ALA* 3.5 4.9 - - - +
3050 VAL* 3.1 33.7 + - + +
3280 ILE* 1.3 74.9 - - - +
3300 ASP* 1.4 67.6 + - - +
3310 LEU* 4.7 0.3 - - - +
3470 GLN* 5.4 1.1 - - - -
3480 ARG 3.4 29.2 - - - +
3490 TYR* 4.0 5.8 - - + +
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Residues in contact with ASP 330 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3030 HIS 4.1 5.8 - - - +
3040 ALA* 4.4 4.9 - - - +
3290 ILE* 1.4 77.4 - - - +
3310 LEU* 1.3 60.6 + - - +
3320 GLY* 3.2 6.7 + - - +
3330 SER 5.6 0.4 - - - +
3360 GLY* 5.8 3.6 - - - -
3370 THR* 4.4 21.8 - - - +
3440 ILE* 5.3 7.3 - - + +
3450 GLU 4.4 8.7 + - - +
3460 PRO* 3.9 25.0 - - + +
3470 GLN* 4.0 14.6 + - - +
3480 ARG 4.8 0.2 + - - -
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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